Merge pull request #194 from AhmedFaisal95/fix/inference-logging

Fix: Inference script logging

FastSurferCNN/run_prediction.py

@@ -293,6 +293,8 @@ def handle_cuda_memory_exception(exception: RuntimeError, exit_on_out_of_memory:
                         help="Name under which the conformed input image will be saved, in the same directory as the segmentation "
                              "(the input image is always conformed first, if it is not already conformed). "
                              "The original input image is saved in the output directory as $id/mri/orig/001.mgz. Default: mri/orig.mgz.")
+    parser.add_argument('--log_name', type=str, dest='log_name', default="",
+                        help="Absolute path to file in which run logs will be saved. If not set, logs will not be saved.")
     parser.add_argument("--out_dir", type=str, default=None,
                         help="Directory in which evaluation results should be written. "
                              "Will be created if it does not exist. Optional if full path is defined for --pred_name.")
@@ -349,8 +351,7 @@ def handle_cuda_memory_exception(exception: RuntimeError, exit_on_out_of_memory:
 
     # Set up logging
     from utils.logging import setup_logging
-    cfg = args2cfg(args)[0]
-    setup_logging(cfg.OUT_LOG_DIR, cfg.OUT_LOG_NAME)
+    setup_logging(args.log_name)
 
     # Download checkpoints if they do not exist
     # see utils/checkpoint.py for default paths

FastSurferCNN/utils/logging.py

@@ -14,28 +14,29 @@
 # limitations under the License.
 
 # IMPORTS
+import os
+
 from logging import *
-from typing import Union as _Union
 from sys import stdout as _stdout
-from pathlib import Path as _Path
-from os import makedirs as _makedirs
-from os.path import join as _join
 
 
-def setup_logging(output_dir: _Union[str, _Path], expr_num: str):
+def setup_logging(log_file_path: str):
     """
     Sets up the logging
     """
     # Set up logging format.
     _FORMAT = "[%(levelname)s: %(filename)s: %(lineno)4d]: %(message)s"
-    log_folder = _join(output_dir, "logs")
-    _makedirs(log_folder, exist_ok=True)
-    log_file = _join(log_folder, f"expr_{expr_num}.log")
+    handlers = [StreamHandler(_stdout)]
+
+    if log_file_path:
+        log_dir_path = os.path.dirname(log_file_path)
+        log_file_name = os.path.basename(log_file_path)
+        if not os.path.exists(log_dir_path):
+            os.makedirs(log_dir_path)
 
-    fh = FileHandler(filename=log_file, mode='a')
-    ch = StreamHandler(_stdout)
+        handlers.append(FileHandler(filename=log_file_path, mode='a'))
 
-    basicConfig(level=INFO, format=_FORMAT, handlers=[fh, ch])
+    basicConfig(level=INFO, format=_FORMAT, handlers=handlers)
 
 # At this point, this is just an alias for compatibility’s sake
 get_logger = getLogger

run_fastsurfer.sh

@@ -443,14 +443,14 @@ if [ "$surf_only" == "0" ]; then
   # "============= Running FastSurferCNN (Creating Segmentation aparc.DKTatlas.aseg.mgz) ==============="
   # use FastSurferCNN to create cortical parcellation + anatomical segmentation into 95 classes.
   mkdir -p "$(dirname "$seg_log")"
-  echo "Log file for fastsurfercnn eval.py" > $seg_log
+  echo "Log file for fastsurfercnn run_prediction.py" > $seg_log
   date  |& tee -a $seg_log
   echo "" |& tee -a $seg_log
 
   pushd $fastsurfercnndir
-  cmd="$python run_prediction.py --orig_name $t1 --pred_name $seg --conf_name $conformed_name $hires --ckpt_sag $weights_sag --ckpt_ax $weights_ax --ckpt_cor $weights_cor --batch_size $batch_size --cfg_cor $config_cor --cfg_ax $config_ax --cfg_sag $config_sag --run_viewagg_on $viewagg --device $device"
+  cmd="$python run_prediction.py --orig_name $t1 --pred_name $seg --conf_name $conformed_name --log_name $seg_log $hires --ckpt_sag $weights_sag --ckpt_ax $weights_ax --ckpt_cor $weights_cor --batch_size $batch_size --cfg_cor $config_cor --cfg_ax $config_ax --cfg_sag $config_sag --run_viewagg_on $viewagg --device $device"
   echo $cmd |& tee -a $seg_log
-  $cmd |& tee -a $seg_log
+  $cmd
   if [ ${PIPESTATUS[0]} -ne 0 ] ; then exit 1 ; fi
   popd
 fi