Use scilpy's add_verbose_arg

dwi_ml/io_utils.py

@@ -5,15 +5,6 @@
 from scilpy.io.utils import add_processes_arg
 
 
-def add_verbose_arg(p):
-    # Can eventually become scilpy.io.utils.add_verbose_arg
-    p.add_argument('-v', default="WARNING", const='INFO', nargs='?',
-                   choices=['DEBUG', 'INFO', 'WARNING'], dest='verbose',
-                   help='Produces verbose output depending on '
-                        'the provided level. \nDefault level is warning, '
-                        'default when using -v is info.')
-
-
 def add_resample_or_compress_arg(p: ArgumentParser):
     g = p.add_mutually_exclusive_group()
     g.add_argument(

dwi_ml/testing/projects/tt_visu_argparser.py

@@ -51,10 +51,10 @@
 """
 import argparse
 
-from scilpy.io.utils import (add_overwrite_arg, add_reference_arg)
+from scilpy.io.utils import (add_overwrite_arg, add_reference_arg,
+                             add_verbose_arg)
 
-from dwi_ml.io_utils import (add_arg_existing_experiment_path,
-                             add_verbose_arg, add_memory_args)
+from dwi_ml.io_utils import add_arg_existing_experiment_path, add_memory_args
 from dwi_ml.testing.utils import add_args_testing_subj_hdf5
 
 

dwi_ml/testing/visu_loss_utils.py

@@ -4,11 +4,11 @@
 import os.path
 from argparse import ArgumentParser
 
-from scilpy.io.utils import (add_overwrite_arg,
+from scilpy.io.utils import (add_overwrite_arg, add_verbose_arg,
                              assert_inputs_exist, assert_outputs_exist,
                              add_reference_arg, ranged_type)
 
-from dwi_ml.io_utils import add_memory_args, add_verbose_arg
+from dwi_ml.io_utils import add_memory_args
 
 
 def prepare_args_visu_loss(p: ArgumentParser):

scripts_python/dwiml_create_hdf5_dataset.py

@@ -25,16 +25,15 @@
 import shutil
 from pathlib import Path
 
-from scilpy.io.utils import (add_overwrite_arg, assert_inputs_exist,
-                             assert_outputs_exist)
+from scilpy.io.utils import (add_overwrite_arg, add_verbose_arg,
+                             assert_inputs_exist, assert_outputs_exist)
 
 from dipy.io.stateful_tractogram import set_sft_logger_level
 
 from dwi_ml.data.hdf5.hdf5_creation import HDF5Creator
 from dwi_ml.data.hdf5.utils import (
     add_hdf5_creation_args, add_streamline_processing_args)
 from dwi_ml.experiment_utils.timer import Timer
-from dwi_ml.io_utils import add_verbose_arg
 
 
 def _initialize_intermediate_subdir(hdf5_file, save_intermediate):

scripts_python/dwiml_visualize_logs.py

@@ -36,9 +36,9 @@
 import matplotlib.pyplot as plt
 import numpy as np
 
-from scilpy.io.utils import assert_outputs_exist, add_overwrite_arg
+from scilpy.io.utils import (add_overwrite_arg, add_verbose_arg,
+                             assert_outputs_exist)
 
-from dwi_ml.io_utils import add_verbose_arg
 from dwi_ml.viz.logs_plots import visualize_logs
 
 

scripts_python/dwiml_visualize_logs_correlation.py

@@ -13,9 +13,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 
-from scilpy.io.utils import add_overwrite_arg
-
-from dwi_ml.io_utils import add_verbose_arg
+from scilpy.io.utils import add_overwrite_arg, add_verbose_arg
 
 
 def _build_arg_parser():

scripts_python/l2t_resume_training_from_checkpoint.py

@@ -9,9 +9,10 @@
 # Importing now to solve issues later.
 import comet_ml
 
+from scilpy.io.utils import add_verbose_arg
+
 from dwi_ml.data.dataset.utils import prepare_multisubjectdataset
 from dwi_ml.experiment_utils.timer import Timer
-from dwi_ml.io_utils import add_verbose_arg
 from dwi_ml.models.projects.learn2track_model import Learn2TrackModel
 from dwi_ml.training.batch_loaders import DWIMLBatchLoaderOneInput
 from dwi_ml.training.batch_samplers import DWIMLBatchIDSampler

scripts_python/l2t_track_from_model.py

@@ -12,9 +12,8 @@
 from dipy.io.utils import is_header_compatible
 import h5py
 import nibabel as nib
-import torch
 
-from scilpy.io.utils import (add_sphere_arg,
+from scilpy.io.utils import (add_sphere_arg, add_verbose_arg,
                              assert_inputs_exist, assert_outputs_exist,
                              verify_compression_th)
 from scilpy.tracking.utils import (add_seeding_options,
@@ -23,7 +22,6 @@
 
 from dwi_ml.experiment_utils.prints import format_dict_to_str
 from dwi_ml.experiment_utils.timer import Timer
-from dwi_ml.io_utils import add_verbose_arg
 from dwi_ml.models.projects.learn2track_model import Learn2TrackModel
 from dwi_ml.testing.utils import prepare_dataset_one_subj, \
     find_hdf5_associated_to_experiment

scripts_python/l2t_train_model.py

@@ -14,12 +14,13 @@
 import comet_ml
 import torch
 
-from scilpy.io.utils import assert_inputs_exist, assert_outputs_exist
+from scilpy.io.utils import (add_verbose_arg, assert_inputs_exist,
+                             assert_outputs_exist)
 
 from dwi_ml.data.dataset.utils import prepare_multisubjectdataset
 from dwi_ml.experiment_utils.prints import format_dict_to_str
 from dwi_ml.experiment_utils.timer import Timer
-from dwi_ml.io_utils import add_verbose_arg, add_memory_args
+from dwi_ml.io_utils import add_memory_args
 from dwi_ml.models.projects.learn2track_model import Learn2TrackModel
 from dwi_ml.models.projects.learn2track_utils import add_model_args
 from dwi_ml.models.utils.direction_getters import check_args_direction_getter

scripts_python/l2t_update_deprecated_exp.py

@@ -12,11 +12,10 @@
 
 import numpy as np
 import torch
-from scilpy.io.utils import add_overwrite_arg
+from scilpy.io.utils import add_overwrite_arg, add_verbose_arg
 
 from dwi_ml.data.dataset.utils import prepare_multisubjectdataset
 from dwi_ml.experiment_utils.prints import format_dict_to_str
-from dwi_ml.io_utils import add_verbose_arg
 from dwi_ml.models.projects.learn2track_model import Learn2TrackModel
 from dwi_ml.training.batch_loaders import DWIMLBatchLoaderOneInput
 from dwi_ml.training.batch_samplers import DWIMLBatchIDSampler

scripts_python/tt_resume_training_from_checkpoint.py

@@ -9,9 +9,11 @@
 # Importing now to solve issues later.
 import comet_ml
 
+from scilpy.io.utils import add_verbose_arg
+
 from dwi_ml.data.dataset.utils import prepare_multisubjectdataset
 from dwi_ml.experiment_utils.timer import Timer
-from dwi_ml.io_utils import add_verbose_arg, verify_which_model_in_path
+from dwi_ml.io_utils import verify_which_model_in_path
 from dwi_ml.models.projects.transformer_models import find_transformer_class
 from dwi_ml.training.batch_loaders import DWIMLBatchLoaderOneInput
 from dwi_ml.training.batch_samplers import DWIMLBatchIDSampler

scripts_python/tt_track_from_model.py

@@ -14,7 +14,7 @@
 import h5py
 import nibabel as nib
 
-from scilpy.io.utils import (add_sphere_arg,
+from scilpy.io.utils import (add_sphere_arg, add_verbose_arg,
                              assert_inputs_exist, assert_outputs_exist,
                              verify_compression_th)
 from scilpy.tracking.utils import (add_seeding_options,
@@ -23,7 +23,7 @@
 
 from dwi_ml.experiment_utils.prints import format_dict_to_str
 from dwi_ml.experiment_utils.timer import Timer
-from dwi_ml.io_utils import add_verbose_arg, verify_which_model_in_path
+from dwi_ml.io_utils import verify_which_model_in_path
 from dwi_ml.models.projects.transformer_models import find_transformer_class
 from dwi_ml.testing.utils import prepare_dataset_one_subj, \
     find_hdf5_associated_to_experiment

scripts_python/tt_train_model.py

@@ -14,14 +14,16 @@
 import comet_ml
 import torch
 
-from scilpy.io.utils import assert_inputs_exist, assert_outputs_exist
+from scilpy.io.utils import (add_verbose_arg, assert_inputs_exist,
+                             assert_outputs_exist)
 
 from dwi_ml.data.dataset.utils import prepare_multisubjectdataset
 from dwi_ml.experiment_utils.prints import format_dict_to_str
 from dwi_ml.experiment_utils.timer import Timer
-from dwi_ml.io_utils import add_memory_args, add_verbose_arg
-from dwi_ml.models.projects.transformer_models import \
-    OriginalTransformerModel, TransformerSrcAndTgtModel, TransformerSrcOnlyModel
+from dwi_ml.io_utils import add_memory_args
+from dwi_ml.models.projects.transformer_models import (
+    OriginalTransformerModel, TransformerSrcAndTgtModel,
+    TransformerSrcOnlyModel)
 from dwi_ml.models.projects.transformers_utils import (
     add_transformers_model_args)
 from dwi_ml.models.utils.direction_getters import check_args_direction_getter
@@ -32,8 +34,8 @@
                                                  prepare_batch_loader)
 from dwi_ml.training.utils.experiment import (
     add_mandatory_args_experiment_and_hdf5_path)
-from dwi_ml.training.utils.trainer import add_training_args, run_experiment, \
-    format_lr
+from dwi_ml.training.utils.trainer import (add_training_args, run_experiment,
+                                           format_lr)
 
 
 def prepare_arg_parser():