Merge pull request #850 from ThoumyreStanislas/add_verbose

[WIP] Add_verbose_arg

scilpy/io/utils.py

@@ -18,6 +18,7 @@
 from PIL import Image
 from scipy.io import loadmat
 import six
+import importlib.metadata
 
 from scilpy.io.streamlines import load_tractogram_with_reference
 from scilpy.gradients.bvec_bval_tools import DEFAULT_B0_THRESHOLD
@@ -876,3 +877,12 @@ def get_default_screenshotting_data(args):
         labelmap_img, \
         mask_imgs, \
         masks_colors
+
+
+def add_scilpy_version(verbose = True):
+
+    version = importlib.metadata.version('scilpy')
+
+    logging.getLogger().setLevel(logging.INFO)
+    logging.info("Scilpy version: {}".format(version))
+

scripts/scil_NODDI_maps.py

@@ -79,8 +79,9 @@ def _build_arg_parser():
                     help='Compute kernels only, --save_kernels must be used.')
 
     add_processes_arg(p)
-    add_overwrite_arg(p)
     add_verbose_arg(p)
+    add_overwrite_arg(p)
+
     return p
 
 

scripts/scil_NODDI_priors.py

@@ -79,8 +79,8 @@ def _build_arg_parser():
                     help='Output path for the ventricule mask.\nIf not set, '
                          'the mask will not be saved.')
 
-    add_overwrite_arg(p)
     add_verbose_arg(p)
+    add_overwrite_arg(p)
 
     return p
 

scripts/scil_aodf_metrics.py

@@ -38,6 +38,7 @@
                                  compute_odd_power_map)
 from scilpy.io.utils import (add_processes_arg,
                              add_sh_basis_args,
+                             add_verbose_arg,
                              assert_inputs_exist,
                              assert_outputs_exist,
                              add_overwrite_arg)
@@ -106,6 +107,7 @@ def _build_arg_parser():
 
     add_processes_arg(p)
     add_sh_basis_args(p)
+    add_verbose_arg(p)
     add_overwrite_arg(p)
     return p
 

scripts/scil_btensor_metrics.py

@@ -102,8 +102,8 @@ def _build_arg_parser():
 
     add_force_b0_arg(p)
     add_processes_arg(p)
-    add_overwrite_arg(p)
     add_verbose_arg(p)
+    add_overwrite_arg(p)
 
     p.add_argument(
         '--not_all', action='store_true',

scripts/scil_bundle_compute_centroid.py

@@ -14,6 +14,7 @@
 from scilpy.io.utils import (add_overwrite_arg,
                              assert_inputs_exist,
                              assert_outputs_exist,
+                             add_verbose_arg,
                              add_reference_arg)
 from scilpy.tractanalysis.features import get_streamlines_centroid
 
@@ -32,6 +33,7 @@ def _build_arg_parser():
                         '[%(default)s].')
 
     add_reference_arg(p)
+    add_verbose_arg(p)
     add_overwrite_arg(p)
     return p
 

scripts/scil_bundle_compute_endpoints_map.py

@@ -23,6 +23,7 @@
 
 from scilpy.io.streamlines import load_tractogram_with_reference
 from scilpy.io.utils import (add_json_args,
+                             add_verbose_arg,
                              add_overwrite_arg,
                              add_reference_arg,
                              assert_inputs_exist,
@@ -53,6 +54,7 @@ def _build_arg_parser():
 
     add_json_args(p)
     add_reference_arg(p)
+    add_verbose_arg(p)
     add_overwrite_arg(p)
 
     return p

scripts/scil_bundle_diameter.py

@@ -40,6 +40,7 @@
 from scilpy.io.utils import (add_overwrite_arg,
                              add_reference_arg,
                              add_json_args,
+                             add_verbose_arg,
                              assert_inputs_exist,
                              assert_output_dirs_exist_and_empty,
                              parser_color_type,
@@ -84,6 +85,7 @@ def _build_arg_parser():
 
     add_reference_arg(p)
     add_json_args(p)
+    add_verbose_arg(p)
     add_overwrite_arg(p)
 
     return p

scripts/scil_bundle_filter_by_occurence.py

@@ -24,6 +24,7 @@
 from scilpy.io.streamlines import load_tractogram_with_reference
 from scilpy.io.utils import (add_overwrite_arg,
                              add_reference_arg,
+                             add_verbose_arg,
                              assert_inputs_exist,
                              assert_outputs_exist)
 from scilpy.tractanalysis.streamlines_metrics import compute_tract_counts_map
@@ -55,6 +56,7 @@ def _build_arg_parser():
                         'as part of the \'gold standard\'. [0.5]')
 
     add_reference_arg(p)
+    add_verbose_arg(p)
     add_overwrite_arg(p)
 
     return p

scripts/scil_bundle_generate_priors.py

@@ -21,6 +21,7 @@
 from scilpy.io.utils import (add_overwrite_arg,
                              add_reference_arg,
                              add_sh_basis_args,
+                             add_verbose_arg,
                              assert_inputs_exist,
                              assert_outputs_exist)
 from scilpy.reconst.utils import find_order_from_nb_coeff
@@ -60,8 +61,9 @@ def _build_arg_parser():
                    help='Output directory for all generated files,\n'
                         'default is current directory.')
 
-    add_overwrite_arg(p)
     add_reference_arg(p)
+    add_verbose_arg(p)
+    add_overwrite_arg(p)
 
     return p
 

scripts/scil_bundle_label_map.py

@@ -30,6 +30,7 @@
 from scilpy.io.streamlines import load_tractogram_with_reference
 from scilpy.io.utils import (add_overwrite_arg,
                              add_reference_arg,
+                             add_verbose_arg,
                              assert_inputs_exist,
                              assert_output_dirs_exist_and_empty)
 from scilpy.tractanalysis.streamlines_metrics import compute_tract_counts_map
@@ -71,6 +72,7 @@ def _build_arg_parser():
                    help='Use the new labelling method (multi-centroids).')
 
     add_reference_arg(p)
+    add_verbose_arg(p)
     add_overwrite_arg(p)
 
     return p

scripts/scil_bundle_mean_fixel_afd.py

@@ -18,7 +18,7 @@
 
 from scilpy.io.streamlines import load_tractogram_with_reference
 from scilpy.io.utils import (add_overwrite_arg, add_sh_basis_args,
-                             add_reference_arg,
+                             add_reference_arg, add_verbose_arg,
                              assert_inputs_exist, assert_outputs_exist)
 from scilpy.tractanalysis.afd_along_streamlines \
     import afd_map_along_streamlines
@@ -48,6 +48,7 @@ def _build_arg_parser():
 
     add_reference_arg(p)
     add_sh_basis_args(p)
+    add_verbose_arg(p)
     add_overwrite_arg(p)
     return p
 

scripts/scil_bundle_mean_fixel_afd_from_hdf5.py

@@ -27,6 +27,7 @@
 from scilpy.io.utils import (add_overwrite_arg,
                              add_processes_arg,
                              add_sh_basis_args,
+                             add_verbose_arg,
                              assert_inputs_exist,
                              assert_outputs_exist,
                              validate_nbr_processes)
@@ -86,6 +87,7 @@ def _build_arg_parser():
 
     add_processes_arg(p)
     add_sh_basis_args(p)
+    add_verbose_arg(p)
     add_overwrite_arg(p)
     return p
 

scripts/scil_bundle_mean_fixel_lobe_metric.py

@@ -31,6 +31,7 @@
 from scilpy.io.streamlines import load_tractogram_with_reference
 from scilpy.io.utils import (add_overwrite_arg,
                              add_reference_arg,
+                             add_verbose_arg,
                              assert_inputs_exist, assert_outputs_exist)
 from scilpy.tractanalysis.lobe_metrics_along_streamlines \
     import lobe_specific_metric_map_along_streamlines
@@ -58,7 +59,9 @@ def _build_arg_parser():
                         'alignment. [%(default)s]')
 
     add_reference_arg(p)
+    add_verbose_arg(p)
     add_overwrite_arg(p)
+
     return p
 
 

scripts/scil_bundle_mean_std.py

@@ -27,7 +27,7 @@
 from scilpy.utils.filenames import split_name_with_nii
 from scilpy.io.streamlines import load_tractogram_with_reference
 from scilpy.io.utils import (add_json_args,
-                             add_reference_arg,
+                             add_reference_arg, add_verbose_arg,
                              assert_inputs_exist, assert_outputs_exist,
                              verify_compatibility_with_reference_sft)
 from scilpy.utils.metrics_tools import get_bundle_metrics_mean_std, \
@@ -68,9 +68,10 @@ def _build_arg_parser():
     p.add_argument('--out_json',
                    help='Path of the output file. If not given, the output '
                         'is simply printed on screen.')
+
     add_reference_arg(p)
     add_json_args(p)
-
+    add_verbose_arg(p)
     return p
 
 

scripts/scil_bundle_pairwise_comparison.py

@@ -37,6 +37,7 @@
                              add_overwrite_arg,
                              add_processes_arg,
                              add_reference_arg,
+                             add_verbose_arg,
                              assert_inputs_exist,
                              assert_outputs_exist,
                              link_bundles_and_reference,
@@ -82,6 +83,7 @@ def _build_arg_parser():
     add_processes_arg(p)
     add_reference_arg(p)
     add_json_args(p)
+    add_verbose_arg(p)
     add_overwrite_arg(p)
 
     return p

scripts/scil_bundle_score_many_bundles_one_tractogram.py

@@ -82,10 +82,10 @@ def _build_arg_parser():
                         "file are considered \nas absolute paths.")
 
     add_json_args(p)
-    add_overwrite_arg(p)
     add_reference_arg(p)
-    add_verbose_arg(p)
     add_bbox_arg(p)
+    add_verbose_arg(p)
+    add_overwrite_arg(p)
 
     return p
 

scripts/scil_bundle_score_same_bundle_many_segmentations.py

@@ -70,8 +70,8 @@ def _build_arg_parser():
 
     add_processes_arg(p)
     add_reference_arg(p)
-    add_verbose_arg(p)
     add_json_args(p)
+    add_verbose_arg(p)
     add_overwrite_arg(p)
 
     return p

scripts/scil_bundle_shape_measures.py

@@ -44,6 +44,7 @@
 import numpy as np
 
 from scilpy.io.utils import (add_json_args,
+                             add_verbose_arg,
                              add_overwrite_arg,
                              add_processes_arg,
                              add_reference_arg,
@@ -85,6 +86,7 @@ def _build_arg_parser():
     add_reference_arg(p)
     add_processes_arg(p)
     add_json_args(p)
+    add_verbose_arg(p)
     add_overwrite_arg(p)
 
     return p

scripts/scil_bundle_volume_per_label.py

@@ -22,6 +22,7 @@
 
 from scilpy.image.labels import get_data_as_labels
 from scilpy.io.utils import (add_json_args,
+                             add_verbose_arg,
                              add_overwrite_arg,
                              assert_inputs_exist)
 
@@ -36,6 +37,7 @@ def _build_arg_parser():
                    help='Bundle name.')
 
     add_json_args(p)
+    add_verbose_arg(p)
     add_overwrite_arg(p)
 
     return p

scripts/scil_clean_qbx_clusters.py

@@ -64,9 +64,9 @@ def _build_arg_parser():
                    help='Linewidth of the current cluster [%(default)s].')
 
     add_reference_arg(p)
-    add_overwrite_arg(p)
-    add_verbose_arg(p)
     add_bbox_arg(p)
+    add_verbose_arg(p)
+    add_overwrite_arg(p)
 
     return p
 

scripts/scil_connectivity_hdf5_average_density_map.py

@@ -28,6 +28,7 @@
 
 from scilpy.io.streamlines import reconstruct_streamlines_from_hdf5
 from scilpy.io.utils import (add_overwrite_arg,
+                             add_verbose_arg,
                              add_processes_arg,
                              assert_inputs_exist,
                              assert_output_dirs_exist_and_empty,
@@ -48,6 +49,7 @@ def _build_arg_parser():
                    help='Binarize density maps before the population average.')
 
     add_processes_arg(p)
+    add_verbose_arg(p)
     add_overwrite_arg(p)
     return p
 

scripts/scil_connectivity_math.py

@@ -54,8 +54,8 @@ def _build_arg_parser():
                    help='Does not affect the background of the original '
                         'matrices.')
 
-    add_overwrite_arg(p)
     add_verbose_arg(p)
+    add_overwrite_arg(p)
 
     return p
 

scripts/scil_connectivity_normalize.py

@@ -50,6 +50,7 @@
     normalize_matrix_from_values, normalize_matrix_from_parcel
 from scilpy.image.volume_math import normalize_max, normalize_sum, base_10_log
 from scilpy.io.utils import (add_overwrite_arg,
+                             add_verbose_arg,
                              assert_inputs_exist,
                              assert_outputs_exist,
                              load_matrix_in_any_format,
@@ -95,6 +96,7 @@ def _build_arg_parser():
     scale.add_argument('--log_10', action='store_true',
                        help='Apply a base 10 logarithm to the matrix.')
 
+    add_verbose_arg(p)
     add_overwrite_arg(p)
 
     return p

scripts/scil_connectivity_pairwise_agreement.py

@@ -15,6 +15,7 @@
 import numpy as np
 
 from scilpy.io.utils import (add_json_args,
+                             add_verbose_arg,
                              add_overwrite_arg,
                              assert_inputs_exist,
                              assert_outputs_exist,
@@ -38,6 +39,7 @@ def _build_arg_parser():
                         'one.')
 
     add_json_args(p)
+    add_verbose_arg(p)
     add_overwrite_arg(p)
 
     return p

scripts/scil_connectivity_print_filenames.py

@@ -22,6 +22,7 @@
 import numpy as np
 
 from scilpy.io.utils import (add_overwrite_arg,
+                             add_verbose_arg,
                              assert_inputs_exist,
                              assert_outputs_exist,
                              load_matrix_in_any_format)
@@ -39,6 +40,7 @@ def _build_arg_parser():
     p.add_argument('out_txt',
                    help='Output text file containing all filenames.')
 
+    add_verbose_arg(p)
     add_overwrite_arg(p)
 
     return p