Merge pull request #647 from frheault/logging_fixes

Fix logging across scilpy

pytest.ini

@@ -0,0 +1,24 @@
+[pytest]
+filterwarnings =
+    default
+    once:::dipy
+    once:::fury
+    ignore:::h5py
+    ignore:::matplotlib
+    ignore:::nibabel
+    ignore:::nilearn
+    ignore:::numpy
+    ignore:::Pillow
+    once:::bids-validator
+    once:::pybids
+    ignore:::scikit-learn
+    ignore:::sklearn
+    ignore:::scipy
+    ignore:::vtk
+    default:::trimeshpy
+    ignore:::nilearn
+    once:::bctpy
+    once:::statsmodels
+    once:::dmri-commit
+    once:::cvxpy
+    once:::dmri-amico

scilpy/utils/image.py

@@ -178,7 +178,7 @@ def compute_snr(dwi, bval, bvec, b0_thr, mask,
         Set to use logging
     """
     if verbose:
-        logging.basicConfig(level=logging.INFO)
+        logging.getLogger().setLevel(logging.INFO)
 
     img = nib.load(dwi)
     data = img.get_fdata(dtype=np.float32)

scripts/scil_apply_transform_to_tractogram.py

@@ -98,7 +98,7 @@ def main():
     args = parser.parse_args()
 
     if args.verbose:
-        logging.basicConfig(level=logging.DEBUG)
+        logging.getLogger().setLevel(logging.DEBUG)
 
     assert_inputs_exist(parser, [args.in_moving_tractogram,
                                  args.in_target_file,

scripts/scil_assign_custom_color_to_tractogram.py

@@ -160,7 +160,7 @@ def save_colorbar(cmap, lbound, ubound, args):
 def main():
     parser = _build_arg_parser()
     args = parser.parse_args()
-    logging.basicConfig(level=logging.WARNING)
+    logging.getLogger().setLevel(logging.WARNING)
 
     assert_inputs_exist(parser, args.in_tractogram)
     assert_outputs_exist(parser, args, args.out_tractogram,

scripts/scil_assign_uniform_color_to_tractograms.py

@@ -61,7 +61,7 @@ def _build_arg_parser():
 def main():
     parser = _build_arg_parser()
     args = parser.parse_args()
-    logging.basicConfig(level=logging.WARNING)
+    logging.getLogger().setLevel(logging.WARNING)
 
     if len(args.in_tractograms) > 1 and args.out_tractogram:
         parser.error('Using multiple inputs, use --out_suffix.')

scripts/scil_clean_qbx_clusters.py

@@ -160,7 +160,7 @@ def keypress_callback(obj, _):
                                            create_dir=True)
 
     if args.verbose:
-        logging.basicConfig(level=logging.INFO)
+        logging.getLogger().setLevel(logging.INFO)
 
     if args.min_cluster_size < 1:
         parser.error('Minimum cluster size must be at least 1.')

scripts/scil_compare_connectivity.py

@@ -127,7 +127,7 @@ def main():
     assert_outputs_exist(parser, args, args.out_pval_matrix)
 
     if args.verbose:
-        logging.basicConfig(level=logging.DEBUG)
+        logging.getLogger().setLevel(logging.DEBUG)
 
     if args.filtering_mask:
         filtering_mask = load_matrix_in_any_format(args.filtering_mask)

scripts/scil_compute_NODDI.py

@@ -109,7 +109,7 @@ def main():
     # COMMIT has some c-level stdout and non-logging print that cannot
     # be easily stopped. Manual redirection of all printed output
     if args.verbose:
-        logging.basicConfig(level=logging.DEBUG)
+        logging.getLogger().setLevel(logging.DEBUG)
         redirected_stdout = redirect_stdout(sys.stdout)
     else:
         f = io.StringIO()

scripts/scil_compute_NODDI_priors.py

@@ -98,10 +98,8 @@ def main():
 
     assert_same_resolution([args.in_AD, args.in_FA, args.in_MD])
 
-    if args.verbose:
-        logging.basicConfig(level=logging.DEBUG)
-    else:
-        logging.basicConfig(level=logging.INFO)
+    log_level = logging.DEBUG if args.verbose else logging.INFO
+    logging.getLogger().setLevel(log_level)
 
     fa_img = nib.load(args.in_FA)
     fa_data = fa_img.get_fdata(dtype=np.float32)

scripts/scil_compute_connectivity.py

@@ -281,10 +281,8 @@ def main():
     assert_inputs_exist(parser, [args.in_hdf5, args.in_labels],
                         args.force_labels_list)
 
-    log_level = logging.WARNING
-    if args.verbose:
-        log_level = logging.INFO
-    logging.basicConfig(level=log_level)
+    log_level = logging.INFO if args.verbose else logging.WARNING
+    logging.getLogger().setLevel(log_level)
     coloredlogs.install(level=log_level)
 
     measures_to_compute = []

scripts/scil_compute_fodf_max_in_ventricles.py

@@ -122,7 +122,7 @@ def main():
                          [args.max_value_output, args.mask_output])
 
     if args.verbose:
-        logging.basicConfig(level=logging.DEBUG)
+        logging.getLogger().setLevel(logging.DEBUG)
 
     # Load input image
     img_fODFs = nib.load(args.in_fodfs)

scripts/scil_compute_freewater.py

@@ -117,7 +117,7 @@ def main():
     # COMMIT has some c-level stdout and non-logging print that cannot
     # be easily stopped. Manual redirection of all printed output
     if args.verbose:
-        logging.basicConfig(level=logging.DEBUG)
+        logging.getLogger().setLevel(logging.DEBUG)
         redirected_stdout = redirect_stdout(sys.stdout)
     else:
         f = io.StringIO()

scripts/scil_compute_lobe_specific_fodf_metrics.py

@@ -78,7 +78,7 @@ def main():
     parser = _build_arg_parser()
     args = parser.parse_args()
     if args.verbose:
-        logging.basicConfig(level=logging.INFO)
+        logging.getLogger().setLevel(logging.INFO)
 
     if not args.not_all:
         args.out_fd = args.out_fd or 'fd.nii.gz'

scripts/scil_compute_local_tracking.py

@@ -156,7 +156,7 @@ def main():
     args = parser.parse_args()
 
     if args.verbose:
-        logging.basicConfig(level=logging.DEBUG)
+        logging.getLogger().setLevel(logging.DEBUG)
 
     assert_inputs_exist(parser, [args.in_odf, args.in_seed, args.in_mask])
     assert_outputs_exist(parser, args, args.out_tractogram)

scripts/scil_compute_local_tracking_dev.py

@@ -137,7 +137,7 @@ def main():
     args = parser.parse_args()
 
     if args.verbose:
-        logging.basicConfig(level=logging.DEBUG)
+        logging.getLogger().setLevel(logging.DEBUG)
 
     if not nib.streamlines.is_supported(args.out_tractogram):
         parser.error('Invalid output streamline file format (must be trk or ' +

scripts/scil_compute_local_tracking_gpu.py

@@ -113,7 +113,7 @@ def main():
     args = parser.parse_args()
 
     if args.verbose:
-        logging.basicConfig(level=logging.INFO)
+        logging.getLogger().setLevel(logging.INFO)
 
     assert_inputs_exist(parser, [args.in_odf, args.in_mask, args.in_seed])
     assert_outputs_exist(parser, args, args.out_tractogram)

scripts/scil_compute_maps_for_particle_filter_tracking.py

@@ -59,7 +59,7 @@ def main():
     args = parser.parse_args()
 
     if args.verbose:
-        logging.basicConfig(level=logging.DEBUG)
+        logging.getLogger().setLevel(logging.DEBUG)
 
     assert_inputs_exist(parser, [args.in_wm, args.in_gm, args.in_csf])
     assert_outputs_exist(parser, args,

scripts/scil_compute_mean_frf.py

@@ -33,7 +33,7 @@ def _build_arg_parser():
 def main():
     parser = _build_arg_parser()
     args = parser.parse_args()
-    logging.basicConfig(level=logging.INFO)
+    logging.getLogger().setLevel(logging.INFO)
 
     assert_inputs_exist(parser, args.frf_files)
     assert_outputs_exist(parser, args, args.mean_frf)

scripts/scil_compute_msmt_fodf.py

@@ -96,7 +96,7 @@ def _build_arg_parser():
 def main():
     parser = _build_arg_parser()
     args = parser.parse_args()
-    logging.basicConfig(level=logging.INFO)
+    logging.getLogger().setLevel(logging.INFO)
 
     if not args.not_all:
         args.wm_out_fODF = args.wm_out_fODF or 'wm_fodf.nii.gz'

scripts/scil_compute_msmt_frf.py

@@ -45,8 +45,8 @@
 def buildArgsParser():
 
     p = argparse.ArgumentParser(
-            description=__doc__,
-            formatter_class=argparse.RawDescriptionHelpFormatter)
+        description=__doc__,
+        formatter_class=argparse.RawDescriptionHelpFormatter)
 
     p.add_argument('in_dwi',
                    help='Path to the input diffusion volume.')
@@ -163,10 +163,8 @@ def main():
     parser = buildArgsParser()
     args = parser.parse_args()
 
-    if args.verbose:
-        logging.basicConfig(level=logging.DEBUG)
-    else:
-        logging.basicConfig(level=logging.INFO)
+    log_level = logging.DEBUG if args.verbose else logging.INFO
+    logging.getLogger().setLevel(log_level)
 
     assert_inputs_exist(parser, [args.in_dwi, args.in_bval, args.in_bvec])
     assert_outputs_exist(parser, args, [args.out_wm_frf, args.out_gm_frf,

scripts/scil_compute_pft.py

@@ -144,7 +144,7 @@ def main():
     args = parser.parse_args()
 
     if args.verbose:
-        logging.basicConfig(level=logging.DEBUG)
+        logging.getLogger().setLevel(logging.DEBUG)
 
     assert_inputs_exist(parser, [args.in_sh, args.in_seed,
                                  args.in_map_include,

scripts/scil_compute_powder_average.py

@@ -14,14 +14,10 @@
 being averaged.
 """
 
-from os.path import splitext
-import re
-
 import argparse
 import logging
 
 import nibabel as nib
-from nibabel.tmpdirs import InTemporaryDirectory
 
 import numpy as np
 
@@ -86,7 +82,7 @@ def main():
     assert_outputs_exist(parser, args, args.out_avg)
 
     if args.verbose:
-        logging.basicConfig(level=logging.DEBUG)
+        logging.getLogger().setLevel(logging.DEBUG)
 
     img = nib.load(args.in_dwi)
     data = img.get_fdata(dtype=np.float32)
@@ -103,7 +99,7 @@ def main():
     bvals, _ = read_bvals_bvecs(args.in_bval, None)
 
     # Select diffusion volumes to average
-    if not(args.shells):
+    if not (args.shells):
         # If no shell given, average all diffusion weighted images
         pwd_avg_idx = np.squeeze(np.where(bvals > 0 + args.b0_thr))
         logging.debug('Calculating powder average from all diffusion'

scripts/scil_compute_qbx.py

@@ -62,7 +62,7 @@ def main():
                                        create_dir=True)
 
     if args.verbose:
-        logging.basicConfig(level=logging.INFO)
+        logging.getLogger().setLevel(logging.INFO)
 
     sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
     streamlines = sft.streamlines

scripts/scil_compute_ssst_fodf.py

@@ -60,7 +60,7 @@ def _build_arg_parser():
 def main():
     parser = _build_arg_parser()
     args = parser.parse_args()
-    logging.basicConfig(level=logging.INFO)
+    logging.getLogger().setLevel(logging.INFO)
 
     assert_inputs_exist(parser, [args.in_dwi, args.in_bval, args.in_bvec,
                                  args.frf_file])

scripts/scil_compute_ssst_frf.py

@@ -87,10 +87,8 @@ def main():
     parser = _build_arg_parser()
     args = parser.parse_args()
 
-    if args.verbose:
-        logging.basicConfig(level=logging.DEBUG)
-    else:
-        logging.basicConfig(level=logging.INFO)
+    log_level = logging.DEBUG if args.verbose else logging.INFO
+    logging.getLogger().setLevel(log_level)
 
     assert_inputs_exist(parser, [args.in_dwi, args.in_bval, args.in_bvec])
     assert_outputs_exist(parser, args, args.frf_file)

scripts/scil_compute_todi.py

@@ -84,7 +84,7 @@ def _build_arg_parser():
 def main():
     parser = _build_arg_parser()
     args = parser.parse_args()
-    logging.basicConfig(level=logging.INFO)
+    logging.getLogger().setLevel(logging.INFO)
 
     assert_inputs_exist(parser, args.in_tractogram,
                         [args.mask, args.reference])

scripts/scil_connectivity_math.py

@@ -87,7 +87,7 @@ def main():
     args = parser.parse_args()
 
     if args.verbose:
-        logging.basicConfig(level=logging.INFO)
+        logging.getLogger().setLevel(logging.INFO)
 
     assert_outputs_exist(parser, args, args.out_matrix)
 

scripts/scil_convert_gradients_fsl_to_mrtrix.py

@@ -38,7 +38,7 @@ def main():
     args = parser.parse_args()
 
     if args.verbose:
-        logging.basicConfig(level=logging.INFO)
+        logging.getLogger().setLevel(logging.INFO)
 
     assert_gradients_filenames_valid(parser, [args.fsl_bval, args.fsl_bvec],
                                      'fsl')

scripts/scil_convert_gradients_mrtrix_to_fsl.py

@@ -36,7 +36,7 @@ def main():
     args = parser.parse_args()
 
     if args.verbose:
-        logging.basicConfig(level=logging.INFO)
+        logging.getLogger().setLevel(logging.INFO)
 
     assert_gradients_filenames_valid(parser, args.mrtrix_enc, 'mrtrix')
     assert_gradients_filenames_valid(parser, [args.fsl_bval, args.fsl_bvec],

scripts/scil_convert_tensors.py

@@ -11,7 +11,7 @@
 import nibabel as nib
 import numpy as np
 
-from scilpy.io.utils import (add_overwrite_arg, add_reference_arg,
+from scilpy.io.utils import (add_overwrite_arg,
                              assert_inputs_exist, assert_outputs_exist)
 from scilpy.reconst.dti import (supported_tensor_formats,
                                 tensor_format_description,

scripts/scil_cut_streamlines.py

@@ -64,7 +64,7 @@ def main():
     args = parser.parse_args()
 
     if args.verbose:
-        logging.basicConfig(level=logging.INFO)
+        logging.getLogger().setLevel(logging.INFO)
 
     assert_inputs_exist(parser, [args.in_tractogram, args.in_mask])
     assert_outputs_exist(parser, args, args.out_tractogram)

scripts/scil_decompose_connectivity.py

@@ -252,10 +252,8 @@ def main():
         assert_output_dirs_exist_and_empty(parser, args, args.out_dir,
                                            create_dir=True)
 
-    log_level = logging.WARNING
-    if args.verbose:
-        log_level = logging.INFO
-    logging.basicConfig(level=log_level)
+    log_level = logging.INFO if args.verbose else logging.WARNING
+    logging.getLogger().setLevel(log_level)
     coloredlogs.install(level=log_level)
     set_sft_logger_level('WARNING')
 

scripts/scil_dilate_labels.py

@@ -70,7 +70,7 @@ def _build_arg_parser():
 def main():
     parser = _build_arg_parser()
     args = parser.parse_args()
-    logging.basicConfig(level=logging.INFO)
+    logging.getLogger().setLevel(logging.INFO)
 
     assert_inputs_exist(parser, args.in_file, optional=args.mask)
     assert_outputs_exist(parser, args, args.out_file)

scripts/scil_evaluate_bundles_binary_classification_measures.py

@@ -148,7 +148,7 @@ def main():
     args = parser.parse_args()
 
     if args.verbose:
-        logging.basicConfig(level=logging.INFO)
+        logging.getLogger().setLevel(logging.INFO)
 
     assert_inputs_exist(parser, args.in_bundles)
     assert_outputs_exist(parser, args, args.out_json)

scripts/scil_evaluate_connectivity_graph_measures.py

@@ -157,7 +157,7 @@ def main():
                                  args.in_conn_matrix])
 
     if args.verbose:
-        logging.basicConfig(level=logging.DEBUG)
+        logging.getLogger().setLevel(logging.DEBUG)
 
     if not args.append_json:
         assert_outputs_exist(parser, args, args.out_json)

scripts/scil_execute_angle_aware_bilateral_filtering.py

@@ -85,7 +85,7 @@ def main():
     parser = _build_arg_parser()
     args = parser.parse_args()
     if args.verbose:
-        logging.basicConfig(level=logging.INFO)
+        logging.getLogger().setLevel(logging.INFO)
 
     # Checking args
     outputs = [args.out_sh]