From a2845e41962f5e624cd84629b77b92bb80e686d9 Mon Sep 17 00:00:00 2001
From: Ishaan Desai <ishaandesai@gmail.com>
Date: Mon, 2 Dec 2024 17:45:39 +0100
Subject: [PATCH] Add CSV logging

---
 micro_manager/micro_manager.py         | 20 ++++++++++++--------
 micro_manager/tools/logging_wrapper.py | 20 ++++++++++++++------
 2 files changed, 26 insertions(+), 14 deletions(-)

diff --git a/micro_manager/micro_manager.py b/micro_manager/micro_manager.py
index 1d4ae50..8457615 100644
--- a/micro_manager/micro_manager.py
+++ b/micro_manager/micro_manager.py
@@ -88,11 +88,11 @@ def __init__(self, config_file: str) -> None:
 
         if self._is_adaptivity_on:
             self._adaptivity_logger = Logger(
-                "Adaptivity", "micro-manager-adaptivity.log", self._rank
+                "Adaptivity", "adaptivity_metrics.csv", self._rank, csv_logger=True
             )
 
             self._adaptivity_logger.log_info_one_rank(
-                "Time,Avg Active Sims,Avg Inactive Sims"
+                "Time,Avg Active Sims,Avg Inactive Sims,Max Active,Max Inactive"
             )
 
             self._number_of_sims_for_adaptivity = 0
@@ -316,12 +316,15 @@ def solve(self) -> None:
                             )
 
                             self._adaptivity_logger.log_info_one_rank(
-                                "{},{},{}".format(
+                                "{},{},{},{},{}".format(
                                     t,
                                     np.mean(global_active_sims),
                                     np.mean(global_inactive_sims),
+                                    np.max(global_active_sims),
+                                    np.max(global_inactive_sims),
                                 )
                             )
+                self._logger.log_info_one_rank("Time window {} converged.".format(n))
 
         self._participant.finalize()
 
@@ -365,9 +368,6 @@ def initialize(self) -> None:
         assert self._mesh_vertex_coords.size != 0, "Macro mesh has no vertices."
 
         self._local_number_of_sims, _ = self._mesh_vertex_coords.shape
-        self._logger.log_info_any_rank(
-            "Number of local micro simulations = {}".format(self._local_number_of_sims)
-        )
 
         if self._local_number_of_sims == 0:
             if self._is_parallel:
@@ -389,6 +389,10 @@ def initialize(self) -> None:
         # Get global number of micro simulations
         self._global_number_of_sims = np.sum(nms_all_ranks)
 
+        self._logger.log_info_one_rank(
+            "Number of micro simulations: {}".format(self._global_number_of_sims)
+        )
+
         if self._is_adaptivity_on:
             for name, is_data_vector in self._adaptivity_data_names.items():
                 if is_data_vector:
@@ -480,7 +484,7 @@ def initialize(self) -> None:
                         "The initialize() method of the Micro simulation has an incorrect number of arguments."
                     )
             except TypeError:
-                self._logger.log_one_rank(
+                self._logger.log_info_one_rank(
                     "The signature of initialize() method of the micro simulation cannot be determined. Trying to determine the signature by calling the method."
                 )
                 # Try to get the signature of the initialize() method, if it is not written in Python
@@ -488,7 +492,7 @@ def initialize(self) -> None:
                     self._micro_sims[0].initialize()
                     is_initial_data_required = False
                 except TypeError:
-                    self._logger.log_one_rank(
+                    self._logger.log_info_one_rank(
                         "The initialize() method of the micro simulation has arguments. Attempting to call it again with initial data."
                     )
                     try:  # Try to call the initialize() method with initial data
diff --git a/micro_manager/tools/logging_wrapper.py b/micro_manager/tools/logging_wrapper.py
index 72c44aa..8ef7c6b 100644
--- a/micro_manager/tools/logging_wrapper.py
+++ b/micro_manager/tools/logging_wrapper.py
@@ -10,7 +10,7 @@ class Logger:
     Provides a logging wrapper for the Micro Manager classes.
     """
 
-    def __init__(self, name, log_file, rank=0, level=logging.INFO):
+    def __init__(self, name, log_file, rank=0, level=logging.INFO, csv_logger=False):
         """
         Set up a logger.
 
@@ -20,8 +20,12 @@ def __init__(self, name, log_file, rank=0, level=logging.INFO):
             Name of the logger.
         log_file : string
             Name of the log file.
+        rank : int, optional
+            Rank of the logger (default is 0).
         level : int, optional
             Logging level (default is logging.INFO).
+        csv_logger : bool, optional
+            If True, the logger will log in CSV format (default is False).
         """
 
         self._rank = rank
@@ -29,11 +33,15 @@ def __init__(self, name, log_file, rank=0, level=logging.INFO):
         handler = logging.FileHandler(log_file)
         handler.setLevel(level)
 
-        formatter = logging.Formatter(
-            "["
-            + str(self._rank)
-            + "] %(asctime)s - %(name)s - %(levelname)s - %(message)s"
-        )
+        if csv_logger:
+            formatter = logging.Formatter("%(message)s")
+        else:
+            formatter = logging.Formatter(
+                "["
+                + str(self._rank)
+                + "] %(asctime)s - %(name)s - %(levelname)s - %(message)s"
+            )
+
         handler.setFormatter(formatter)
 
         self._logger = logging.getLogger(name)