set up file logger with timestamp

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\

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(

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. "

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

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):

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

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")

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")

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")

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):

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):

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:

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"):

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):

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)"

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):

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),

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 =\

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)