From 0b111ad5c59e964c657da47211f84f59a9bf76f7 Mon Sep 17 00:00:00 2001
From: Pierre Nedelec <65797646+pierre-nedelec@users.noreply.github.com>
Date: Wed, 26 Oct 2022 17:02:20 -0700
Subject: [PATCH 1/3] set up file logger with timestamp

---
 AFQ/api/bundle_dict.py                  |  2 +-
 AFQ/api/participant.py                  |  2 +-
 AFQ/data/fetch.py                       | 12 ++++----
 AFQ/definitions/mapping.py              |  2 +-
 AFQ/segmentation.py                     |  2 +-
 AFQ/tasks/decorators.py                 |  3 +-
 AFQ/tasks/mapping.py                    |  2 +-
 AFQ/tasks/segmentation.py               |  2 +-
 AFQ/tasks/tractography.py               |  2 +-
 AFQ/tasks/viz.py                        |  2 +-
 AFQ/tractography.py                     |  2 +-
 AFQ/utils/bin.py                        |  3 ++
 AFQ/utils/volume.py                     |  2 +-
 AFQ/viz/fury_backend.py                 |  2 +-
 AFQ/viz/plot.py                         |  2 +-
 AFQ/viz/plotly_backend.py               |  2 +-
 AFQ/viz/utils.py                        |  2 +-
 bin/pyAFQ                               | 41 ++++++++++++++++---------
 examples/plot_callosal_tract_profile.py |  2 +-
 19 files changed, 52 insertions(+), 37 deletions(-)

diff --git a/AFQ/api/bundle_dict.py b/AFQ/api/bundle_dict.py
index 6fa72d404..bcc9a9788 100644
--- a/AFQ/api/bundle_dict.py
+++ b/AFQ/api/bundle_dict.py
@@ -168,7 +168,7 @@ def __init__(self,
             for bundle_name in bundle_info:
                 self.bundle_names.append(bundle_name)
 
-        self.logger = logging.getLogger('AFQ')
+        self.logger = logging.getLogger(__name__)
 
         if self.seg_algo == "afq":
             if "FP" in self.bundle_names\
diff --git a/AFQ/api/participant.py b/AFQ/api/participant.py
index 2ac788343..8ff885366 100644
--- a/AFQ/api/participant.py
+++ b/AFQ/api/participant.py
@@ -88,7 +88,7 @@ def __init__(self,
                 "unrecognized parameter tractography_params, "
                 "did you mean tracking_params ?"))
 
-        self.logger = logging.getLogger('AFQ')
+        self.logger = logging.getLogger(__name__)
         self.output_dir = output_dir
 
         self.kwargs = dict(
diff --git a/AFQ/data/fetch.py b/AFQ/data/fetch.py
index d9fef8047..567897b72 100644
--- a/AFQ/data/fetch.py
+++ b/AFQ/data/fetch.py
@@ -163,7 +163,7 @@ def read_callosum_templates(as_img=True, resample_to=False):
     dict with: keys: names of template ROIs and values: nibabel Nifti1Image
     objects from each of the ROI nifti files.
     """
-    logger = logging.getLogger('AFQ')
+    logger = logging.getLogger(__name__)
 
     logger.debug('loading callosum templates')
     tic = time.perf_counter()
@@ -555,7 +555,7 @@ def read_templates(as_img=True, resample_to=False):
     dict with: keys: names of template ROIs and values: nibabel Nifti1Image
     objects from each of the ROI nifti files.
     """
-    logger = logging.getLogger('AFQ')
+    logger = logging.getLogger(__name__)
     logger.debug('loading AFQ templates')
     tic = time.perf_counter()
 
@@ -649,7 +649,7 @@ def read_or_templates(as_img=True, resample_to=False):
     dict with: keys: names of template ROIs and values: nibabel Nifti1Image
     objects from each of the ROI nifti files.
     """
-    logger = logging.getLogger('AFQ')
+    logger = logging.getLogger(__name__)
 
     logger.debug('loading or templates')
     tic = time.perf_counter()
@@ -795,7 +795,7 @@ def organize_stanford_data(path=None, clear_previous_afq=False):
     If clear_previous_afq is True and there is an afq folder in derivatives,
     it will be removed.
     """
-    logger = logging.getLogger('AFQ')
+    logger = logging.getLogger(__name__)
 
     # fetches data for first subject and session
     logger.info('fetching Stanford HARDI data')
@@ -1196,7 +1196,7 @@ def bundles_to_aal(bundles, atlas=None):
                     targets[bundle + "_" + region_name] = nib.Nifti1Image(
                         aal_roi, atlas.affine)
         else:
-            logger = logging.getLogger('AFQ')
+            logger = logging.getLogger(__name__)
             logger.warning(f"Segmentation end points undefined for {bundle},"
                            + " continuing without end points")
             targets[bundle + "_start"] = None
@@ -1317,7 +1317,7 @@ def read_ukbb_fa_template(mask=True):
     )
 
     if not op.exists(fa_path):
-        logger = logging.getLogger('AFQ')
+        logger = logging.getLogger(__name__)
         logger.warning(
             "Downloading brain MRI group mean statistics from UK Biobank. "
             + "This download is approximately 1.1 GB. "
diff --git a/AFQ/definitions/mapping.py b/AFQ/definitions/mapping.py
index 2d2a15a1c..8d5623801 100644
--- a/AFQ/definitions/mapping.py
+++ b/AFQ/definitions/mapping.py
@@ -29,7 +29,7 @@
 __all__ = ["FnirtMap", "SynMap", "SlrMap", "AffMap", "ItkMap"]
 
 
-logger = logging.getLogger('AFQ')
+logger = logging.getLogger(__name__)
 
 
 # For map defintions, get_for_subses should return only the mapping
diff --git a/AFQ/segmentation.py b/AFQ/segmentation.py
index 7f852ebb2..5d945bbb5 100644
--- a/AFQ/segmentation.py
+++ b/AFQ/segmentation.py
@@ -28,7 +28,7 @@
 __all__ = ["Segmentation", "clean_bundle", "clean_by_endpoints"]
 
 
-logger = logging.getLogger('AFQ')
+logger = logging.getLogger(__name__)
 
 
 def _resample_tg(tg, n_points):
diff --git a/AFQ/tasks/decorators.py b/AFQ/tasks/decorators.py
index 40a395af2..8eedcc322 100644
--- a/AFQ/tasks/decorators.py
+++ b/AFQ/tasks/decorators.py
@@ -19,8 +19,7 @@
 __all__ = ["as_file", "as_fit_deriv", "as_img"]
 
 
-logger = logging.getLogger('AFQ')
-logger.setLevel(logging.INFO)
+logger = logging.getLogger(__name__)
 
 
 # get args and kwargs from function
diff --git a/AFQ/tasks/mapping.py b/AFQ/tasks/mapping.py
index 95b75a64f..ff0133ff3 100644
--- a/AFQ/tasks/mapping.py
+++ b/AFQ/tasks/mapping.py
@@ -19,7 +19,7 @@
 from dipy.io.stateful_tractogram import Space
 
 
-logger = logging.getLogger('AFQ')
+logger = logging.getLogger(__name__)
 
 
 @pimms.calc("b0_warped")
diff --git a/AFQ/tasks/segmentation.py b/AFQ/tasks/segmentation.py
index e5b48ecad..8e14347e3 100644
--- a/AFQ/tasks/segmentation.py
+++ b/AFQ/tasks/segmentation.py
@@ -24,7 +24,7 @@
 from dipy.tracking.streamline import set_number_of_points, values_from_volume
 
 
-logger = logging.getLogger('AFQ')
+logger = logging.getLogger(__name__)
 
 
 @pimms.calc("bundles")
diff --git a/AFQ/tasks/tractography.py b/AFQ/tasks/tractography.py
index 25ddd9478..af8dffff3 100644
--- a/AFQ/tasks/tractography.py
+++ b/AFQ/tasks/tractography.py
@@ -11,7 +11,7 @@
 from AFQ.tasks.utils import get_default_args
 from AFQ.definitions.image import ScalarImage
 
-logger = logging.getLogger('AFQ')
+logger = logging.getLogger(__name__)
 
 
 @pimms.calc("seed")
diff --git a/AFQ/tasks/viz.py b/AFQ/tasks/viz.py
index 5a21d6469..cf71b77d7 100644
--- a/AFQ/tasks/viz.py
+++ b/AFQ/tasks/viz.py
@@ -17,7 +17,7 @@
 
 from plotly.subplots import make_subplots
 
-logger = logging.getLogger('AFQ')
+logger = logging.getLogger(__name__)
 
 
 def _viz_prepare_vol(vol, xform, mapping, scalar_dict):
diff --git a/AFQ/tractography.py b/AFQ/tractography.py
index 9cc2fca2a..edf30af56 100644
--- a/AFQ/tractography.py
+++ b/AFQ/tractography.py
@@ -99,7 +99,7 @@ def track(params_file, directions="prob", max_angle=30., sphere=None,
         Descoteaux, M. Towards quantitative connectivity analysis: reducing
         tractography biases. NeuroImage, 98, 266-278, 2014.
     """
-    logger = logging.getLogger('AFQ')
+    logger = logging.getLogger(__name__)
 
     logger.info("Loading Image...")
     if isinstance(params_file, str):
diff --git a/AFQ/utils/bin.py b/AFQ/utils/bin.py
index 33273c5c5..c9b63e0b2 100644
--- a/AFQ/utils/bin.py
+++ b/AFQ/utils/bin.py
@@ -3,6 +3,8 @@
 import platform
 import os.path as op
 import os
+import logging
+logger = logging.getLogger(__name__)
 
 from argparse import ArgumentParser
 from funcargparse import FuncArgParser
@@ -298,6 +300,7 @@ def parse_config_run_afq(toml_file, default_arg_dict, to_call="export_all",
     with open(afq_metadata_file, 'w') as ff:
         ff.write(dict_to_toml(default_arg_dict))
 
+    logger.info("Starting to create the GroupAFQ object")
     myafq = GroupAFQ(bids_path, **kwargs)
 
     # call user specified function:
diff --git a/AFQ/utils/volume.py b/AFQ/utils/volume.py
index 95e770da2..5d29ee1d3 100644
--- a/AFQ/utils/volume.py
+++ b/AFQ/utils/volume.py
@@ -11,7 +11,7 @@
 from dipy.tracking.streamline import select_random_set_of_streamlines
 import dipy.tracking.utils as dtu
 
-logger = logging.getLogger('AFQ')
+logger = logging.getLogger(__name__)
 
 
 def transform_inverse_roi(roi, mapping, bundle_name="ROI"):
diff --git a/AFQ/viz/fury_backend.py b/AFQ/viz/fury_backend.py
index d2e61e6d7..5fbe9b1ef 100644
--- a/AFQ/viz/fury_backend.py
+++ b/AFQ/viz/fury_backend.py
@@ -15,7 +15,7 @@
 except (ImportError, ModuleNotFoundError):
     raise ImportError(vut.viz_import_msg_error("fury"))
 
-viz_logger = logging.getLogger("AFQ")
+viz_logger = logging.getLogger(__name__)
 
 
 def _inline_interact(scene, inline, interact):
diff --git a/AFQ/viz/plot.py b/AFQ/viz/plot.py
index cb1fbdabe..0c8447abc 100644
--- a/AFQ/viz/plot.py
+++ b/AFQ/viz/plot.py
@@ -334,7 +334,7 @@ def __init__(self, out_folder, csv_fnames, names, is_special="",
             Can be 'ICC1, 'ICC2', 'ICC3', 'ICC1k', 'ICC2k', 'ICC3k'.
             Default: "ICC2"
         """
-        self.logger = logging.getLogger('AFQ')
+        self.logger = logging.getLogger(__name__)
         self.ICC_func = ICC_func
         if "k" in self.ICC_func:
             self.ICC_func_name = f"ICC({self.ICC_func[3]},k)"
diff --git a/AFQ/viz/plotly_backend.py b/AFQ/viz/plotly_backend.py
index 84ac63fad..2d0f90da1 100644
--- a/AFQ/viz/plotly_backend.py
+++ b/AFQ/viz/plotly_backend.py
@@ -21,7 +21,7 @@
 
 
 scope = pio.kaleido.scope
-viz_logger = logging.getLogger("AFQ")
+viz_logger = logging.getLogger(__name__)
 
 
 def _inline_interact(figure, show, show_inline):
diff --git a/AFQ/viz/utils.py b/AFQ/viz/utils.py
index 0907a5c41..139ead293 100644
--- a/AFQ/viz/utils.py
+++ b/AFQ/viz/utils.py
@@ -18,7 +18,7 @@
 
 __all__ = ["Viz"]
 
-viz_logger = logging.getLogger("AFQ")
+viz_logger = logging.getLogger(__name__)
 tableau_20 = [
     (0.12156862745098039, 0.4666666666666667, 0.7058823529411765),
     (0.6823529411764706, 0.7803921568627451, 0.9098039215686274),
diff --git a/bin/pyAFQ b/bin/pyAFQ
index b2bf70960..97788e199 100644
--- a/bin/pyAFQ
+++ b/bin/pyAFQ
@@ -1,21 +1,8 @@
 #!/usr/bin/env python
-
 import warnings
 import os.path as op
 from argparse import ArgumentParser
-
-
-with warnings.catch_warnings():
-    warnings.simplefilter("ignore")
-
-    print("Loading AFQ libraries...")
-
-    import AFQ
-    import AFQ.utils.bin as afb
-
-    import logging
-    logger = logging.getLogger('AFQ')
-    logger.setLevel(level=logging.INFO)
+import logging
 
 usage = \
     """pyAFQ /path/to/afq_config.toml
@@ -97,6 +84,10 @@ def parse_cli(arg_dict):
     cli_parser.add_argument(
         '-t', '--notrack', action="store_true", default=False,
         help="Disable the use of pyAFQ being recorded by Google Analytics. ")
+    
+    cli_parser.add_argument(
+        '-l', '--log', default=None,
+        help="Path to log file to save the outputs of pyAFQ.")
 
     opts = cli_parser.parse_args()
 
@@ -109,12 +100,34 @@ def parse_cli(arg_dict):
             "flag when using the pyAFQ CLI")
         import popylar
         popylar.track_event(AFQ._ga_id, "pyAFQ_cli", "CLI called")
+        
+    if opts.log is not None:
+        # Create handler
+        f_handler = logging.FileHandler(opts.log)
+        f_handler.setLevel(logging.INFO)
+        # Create formatter and add it to handler
+        f_format = logging.Formatter(
+            '%(asctime)s - %(name)s:%(levelname)s:%(message)s')
+        f_handler.setFormatter(f_format)
+        # Add handler to the logger
+        logger.addHandler(f_handler)
+        print(f'Logging to file: {opts.log}')
+        logger.info("Starting pyAFQ")
 
     return opts.config, opts.generate_toml, opts.overwrite,\
         opts.verbose, opts.dry_run, opts.to_call, opts.generate_json
 
 
 if __name__ == '__main__':
+    logger = logging.getLogger()
+    logger.setLevel(level=logging.INFO)
+
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore")
+        print("Loading AFQ libraries...")
+        # import AFQ
+        import AFQ.utils.bin as afb
+    
     arg_dict = afb.func_dict_to_arg_dict(logger=logger)
     config_file, generate_only, overwrite, verbose,\
         dry_run, to_call, generate_json =\
diff --git a/examples/plot_callosal_tract_profile.py b/examples/plot_callosal_tract_profile.py
index 3acc634f3..4fa3fbeb3 100644
--- a/examples/plot_callosal_tract_profile.py
+++ b/examples/plot_callosal_tract_profile.py
@@ -50,7 +50,7 @@
 # Ensure segmentation logging information is included in this example's output
 root = logging.getLogger()
 root.setLevel(logging.ERROR)
-logging.getLogger('AFQ').setLevel(logging.INFO)
+logging.getLogger(__name__).setLevel(logging.INFO)
 handler = logging.StreamHandler(sys.stdout)
 handler.setLevel(logging.INFO)
 root.addHandler(handler)

From 551b12579651a9dfea5fd6cae3d1331410cac205 Mon Sep 17 00:00:00 2001
From: Pierre Nedelec <65797646+pierre-nedelec@users.noreply.github.com>
Date: Tue, 10 Jan 2023 22:19:47 -0800
Subject: [PATCH 2/3] custom output directory (instead of default "afq")

---
 AFQ/utils/bin.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/AFQ/utils/bin.py b/AFQ/utils/bin.py
index c9b63e0b2..532bb880d 100644
--- a/AFQ/utils/bin.py
+++ b/AFQ/utils/bin.py
@@ -295,8 +295,12 @@ def parse_config_run_afq(toml_file, default_arg_dict, to_call="export_all",
 
     afq_path = op.join(bids_path, 'derivatives', 'afq')
     os.makedirs(afq_path, exist_ok=True)
-
-    afq_metadata_file = op.join(afq_path, 'afq_metadata.toml')
+    if kwargs['output_dir'] != '':
+        output_dir = kwargs['output_dir']
+        os.makedirs(output_dir, exist_ok=True)
+    else:
+        output_dir = afq_path
+    afq_metadata_file = op.join(output_dir, 'afq_metadata.toml')
     with open(afq_metadata_file, 'w') as ff:
         ff.write(dict_to_toml(default_arg_dict))
 

From 482c9f090b29ba425d782a1826e778f557d398b2 Mon Sep 17 00:00:00 2001
From: Pierre Nedelec <65797646+pierre-nedelec@users.noreply.github.com>
Date: Tue, 10 Jan 2023 22:37:48 -0800
Subject: [PATCH 3/3] logging setup from GroupAFQ

---
 AFQ/api/group.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/AFQ/api/group.py b/AFQ/api/group.py
index 6ba04a303..b4850d0f1 100644
--- a/AFQ/api/group.py
+++ b/AFQ/api/group.py
@@ -42,9 +42,7 @@
 
 __all__ = ["GroupAFQ"]
 
-
-logger = logging.getLogger('AFQ')
-logger.setLevel(logging.INFO)
+logger = logging.getLogger(__name__)
 
 
 # get rid of unnecessary columns in df
@@ -65,6 +63,7 @@ def __init__(self,
                  output_dir=None,
                  parallel_params={"engine": "serial"},
                  bids_layout_kwargs={},
+                 log_level=logging.INFO,
                  **kwargs):
         '''
         Initialize a GroupAFQ object from a BIDS dataset.
@@ -117,6 +116,7 @@ def __init__(self,
             my_path,
             reg_template_spec="mni_t2", reg_subject_spec="b0")
         '''
+        logger.setLevel(log_level)
         if not isinstance(bids_path, str):
             raise TypeError("bids_path must be a string")
         if not op.exists(bids_path):