Add Sciply version - part 3

scripts/scil_gradients_validate_sampling.py

@@ -24,6 +24,13 @@
 optimal b-vectors on a single shell and then saves them as png. Use one or the
 other, not both. For more options on visualization, please use
 scil_viz_gradients_screenshot.py.
+------------------------------------------------------------------------------
+Reference:
+[1] Emmanuel Caruyer, Christophe Lenglet, Guillermo Sapiro,
+    Rachid Deriche. Design of multishell gradient sampling with uniform coverage
+    in diffusion MRI. Magnetic Resonance in Medicine, Wiley, 2013, 69 (6),
+    pp. 1534-1540. <http://dx.doi.org/10.1002/mrm.24736>
+------------------------------------------------------------------------------
 """
 
 import argparse
@@ -45,21 +52,14 @@
 from scilpy.gradients.gen_gradient_sampling import (generate_gradient_sampling,
                                                     energy_comparison)
 from scilpy.viz.gradients import (plot_proj_shell, build_ms_from_shell_idx)
-
-
-EPILOG = """
-References: [1] Emmanuel Caruyer, Christophe Lenglet, Guillermo Sapiro,
-Rachid Deriche. Design of multishell gradient sampling with uniform coverage
-in diffusion MRI. Magnetic Resonance in Medicine, Wiley, 2013, 69 (6),
-pp. 1534-1540. <http://dx.doi.org/10.1002/mrm.24736>
-    """
+from scilpy.version import version_string
 
 
 def _build_arg_parser():
-    p = argparse.ArgumentParser(
-        formatter_class=argparse.RawTextHelpFormatter,
-        description=__doc__,
-        epilog=EPILOG)
+    p = argparse.ArgumentParser(description=__doc__,
+                                formatter_class=argparse.RawTextHelpFormatter,
+                                epilog=version_string)
+
     p.add_argument('in_gradients', nargs='+',
                    help='Path(s) to the gradient file(s). Either FSL '
                         '(.bval, .bvec) or MRtrix (.b).')

scripts/scil_plot_stats_per_point.py

@@ -22,11 +22,14 @@
                              assert_output_dirs_exist_and_empty,
                              add_verbose_arg)
 from scilpy.viz.plot import plot_metrics_stats
+from scilpy.version import version_string
 
 
 def _build_arg_parser():
     p = argparse.ArgumentParser(description=__doc__,
-                                formatter_class=argparse.RawTextHelpFormatter)
+                                formatter_class=argparse.RawTextHelpFormatter,
+                                epilog=version_string)
+
     p.add_argument('in_json',
                    help='JSON file containing the mean/std per point. For '
                         'example, can be created using '

scripts/scil_qball_metrics.py

@@ -39,14 +39,17 @@
                              assert_inputs_exist, assert_outputs_exist,
                              parse_sh_basis_arg, validate_nbr_processes,
                              assert_headers_compatible)
+from scilpy.version import version_string
 
 
 DEFAULT_SMOOTH = 0.006
 
 
 def _build_arg_parser():
-    p = argparse.ArgumentParser(
-        description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
+    p = argparse.ArgumentParser(description=__doc__,
+                                formatter_class=argparse.RawTextHelpFormatter,
+                                epilog=version_string)
+
     p.add_argument('in_dwi',
                    help='Path of the input diffusion volume.')
     p.add_argument('in_bval',

scripts/scil_rgb_convert.py

@@ -30,12 +30,13 @@
 
 from scilpy.io.utils import (add_overwrite_arg, assert_inputs_exist,
                              assert_outputs_exist, add_verbose_arg)
+from scilpy.version import version_string
 
 
 def _build_arg_parser():
-    p = argparse.ArgumentParser(
-        formatter_class=argparse.RawTextHelpFormatter,
-        description=__doc__)
+    p = argparse.ArgumentParser(description=__doc__,
+                                formatter_class=argparse.RawTextHelpFormatter,
+                                epilog=version_string)
 
     p.add_argument('in_image',
                    help='name of input RGB image.\n' +

scripts/scil_search_keywords.py

@@ -64,11 +64,13 @@
 )
 from scilpy.utils.scilpy_bot import SPACING_LEN, VOCAB_FILE_PATH
 from scilpy.io.utils import add_verbose_arg
+from scilpy.version import version_string
 
 
 def _build_arg_parser():
     p = argparse.ArgumentParser(description=__doc__,
-                                formatter_class=argparse.RawTextHelpFormatter)
+                                formatter_class=argparse.RawTextHelpFormatter,
+                                epilog=version_string)
 
     p.add_argument('expressions', nargs='+',
                    help='Search the provided list of expressions.\n'

scripts/scil_sh_convert.py

@@ -23,11 +23,13 @@
                              add_processes_arg, add_verbose_arg,
                              assert_inputs_exist, assert_outputs_exist,
                              parse_sh_basis_arg)
+from scilpy.version import version_string
 
 
 def _build_arg_parser():
-    p = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
-                                description=__doc__)
+    p = argparse.ArgumentParser(description=__doc__,
+                                formatter_class=argparse.RawTextHelpFormatter,
+                                epilog=version_string)
 
     p.add_argument('in_sh',
                    help='Input SH filename. (nii or nii.gz)')

scripts/scil_sh_fusion.py

@@ -12,6 +12,18 @@
 Based on [1] and [2].
 
 Formerly: scil_merge_sh.py
+---------------------------------------------------------------------------------
+References:
+[1] Garyfallidis, E., Zucchelli, M., Houde, J-C., Descoteaux, M.
+    How to perform best ODF reconstruction from the Human Connectome
+    Project sampling scheme?
+    ISMRM 2014.
+
+[2] Khachaturian, M. H., Wisco, J. J., & Tuch, D. S. (2007). Boosting the
+    sampling efficiency of q‐ball imaging using multiple wavevector fusion.
+    Magnetic Resonance in Medicine: An Official Journal of the International
+    Society for Magnetic Resonance in Medicine, 57(2), 289-296.
+---------------------------------------------------------------------------------
 """
 
 import argparse
@@ -23,25 +35,13 @@
 from scilpy.io.image import assert_same_resolution
 from scilpy.io.utils import (add_overwrite_arg, assert_inputs_exist,
                              assert_outputs_exist, add_verbose_arg)
-
-
-EPILOG = """
-Reference:
-[1] Garyfallidis, E., Zucchelli, M., Houde, J-C., Descoteaux, M.
-    How to perform best ODF reconstruction from the Human Connectome
-    Project sampling scheme?
-    ISMRM 2014.
-
-[2] Khachaturian, M. H., Wisco, J. J., & Tuch, D. S. (2007). Boosting the
-    sampling efficiency of q‐ball imaging using multiple wavevector fusion.
-    Magnetic Resonance in Medicine: An Official Journal of the International
-    Society for Magnetic Resonance in Medicine, 57(2), 289-296.
-"""
+from scilpy.version import version_string
 
 
 def _build_arg_parser():
-    p = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
-                                description=__doc__, epilog=EPILOG)
+    p = argparse.ArgumentParser(description=__doc__,
+                                formatter_class=argparse.RawTextHelpFormatter,
+                                epilog=version_string)
 
     p.add_argument('in_shs', nargs="+",
                    help='List of SH files.')

scripts/scil_sh_to_aodf.py

@@ -13,6 +13,16 @@
 Make sure you have pyopencl installed before using this option. By default, the
 OpenCL program will run on the cpu. To use a gpu instead, also specify the
 option --device gpu.
+----------------------------------------------------------------------------------
+References:
+[1] Poirier and Descoteaux, 2024, "A Unified Filtering Method for Estimating
+    Asymmetric Orientation Distribution Functions", Neuroimage, vol. 287,
+    https://doi.org/10.1016/j.neuroimage.2024.120516
+
+[2] Poirier et al, 2021, "Investigating the Occurrence of Asymmetric Patterns
+    in White Matter Fiber Orientation Distribution Functions", ISMRM 2021
+    (abstract 0865)
+---------------------------------------------------------------------------------
 """
 
 import argparse
@@ -28,22 +38,14 @@
                              assert_inputs_exist, add_sh_basis_args,
                              assert_outputs_exist, parse_sh_basis_arg)
 from scilpy.denoise.asym_filtering import (cosine_filtering, unified_filtering)
-
-
-EPILOG = """
-[1] Poirier and Descoteaux, 2024, "A Unified Filtering Method for Estimating
-    Asymmetric Orientation Distribution Functions", Neuroimage, vol. 287,
-    https://doi.org/10.1016/j.neuroimage.2024.120516
-
-[2] Poirier et al, 2021, "Investigating the Occurrence of Asymmetric Patterns
-    in White Matter Fiber Orientation Distribution Functions", ISMRM 2021
-    (abstract 0865)
-"""
+from scilpy.version import version_string
 
 
 def _build_arg_parser():
-    p = argparse.ArgumentParser(description=__doc__, epilog=EPILOG,
-                                formatter_class=argparse.RawTextHelpFormatter)
+    p = argparse.ArgumentParser(description=__doc__,
+                                formatter_class=argparse.RawTextHelpFormatter,
+                                epilog=version_string)
+
     p.add_argument('in_sh',
                    help='Path to the input file.')
 

scripts/scil_sh_to_rish.py

@@ -13,11 +13,13 @@
 
 Each RISH feature will be saved as a separate file.
 
-[1] Mirzaalian, Hengameh, et al. "Harmonizing diffusion MRI data across
-multiple sites and scanners." MICCAI 2015.
-https://scholar.harvard.edu/files/hengameh/files/miccai2015.pdf
-
 Formerly: scil_compute_rish_from_sh.py
+-----------------------------------------------------------------------
+Reference:
+[1] Mirzaalian, Hengameh, et al. "Harmonizing diffusion MRI data across
+    multiple sites and scanners." MICCAI 2015.
+    https://scholar.harvard.edu/files/hengameh/files/miccai2015.pdf
+-----------------------------------------------------------------------
 """
 import argparse
 import logging
@@ -31,11 +33,14 @@
                              assert_outputs_exist, add_verbose_arg,
                              assert_headers_compatible)
 from scilpy.reconst.sh import compute_rish
+from scilpy.version import version_string
 
 
 def _build_arg_parser():
-    p = argparse.ArgumentParser(
-        description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
+    p = argparse.ArgumentParser(description=__doc__,
+                                formatter_class=argparse.RawTextHelpFormatter,
+                                epilog=version_string)
+
     p.add_argument('in_sh',
                    help='Path of the sh image. They can be formatted in any '
                         'sh basis, but we \nexpect it to be a symmetrical '

scripts/scil_sh_to_sf.py

@@ -29,11 +29,14 @@
                              assert_inputs_exist, assert_outputs_exist,
                              parse_sh_basis_arg, validate_nbr_processes)
 from scilpy.reconst.sh import convert_sh_to_sf
+from scilpy.version import version_string
 
 
 def _build_arg_parser():
-    p = argparse.ArgumentParser(
-        description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
+    p = argparse.ArgumentParser(description=__doc__,
+                                formatter_class=argparse.RawTextHelpFormatter,
+                                epilog=version_string)
+
     p.add_argument('in_sh',
                    help='Path of the SH volume.')
     p.add_argument('out_sf',

scripts/scil_stats_group_comparison.py

@@ -56,12 +56,13 @@
                                 get_group_data_sample,
                                 visualise_distribution,
                                 write_current_dictionnary)
+from scilpy.version import version_string
 
 
 def _build_arg_parser():
-
-    p = argparse.ArgumentParser(
-        description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
+    p = argparse.ArgumentParser(description=__doc__,
+                                formatter_class=argparse.RawTextHelpFormatter,
+                                epilog=version_string)
 
     p.add_argument('in_json', metavar='IN_JSON',
                    help='Input JSON file from tractometry nextflow pipeline'

scripts/scil_surface_apply_transform.py

@@ -18,6 +18,11 @@
 (aligned over the b0 in MI-Brain).
 
 Formerly: scil_apply_transform_to_surface.py.
+-------------------------------------------------------------------
+Reference:
+[1] St-Onge, E., Daducci, A., Girard, G. and Descoteaux, M. 2018.
+    Surface-enhanced tractography (SET). NeuroImage.
+-------------------------------------------------------------------
 """
 
 import argparse
@@ -33,18 +38,13 @@
                              assert_outputs_exist,
                              load_matrix_in_any_format)
 from scilpy.surfaces.surface_operations import apply_transform
-
-
-EPILOG = """
-References:
-[1] St-Onge, E., Daducci, A., Girard, G. and Descoteaux, M. 2018.
-    Surface-enhanced tractography (SET). NeuroImage.
-"""
+from scilpy.version import version_string
 
 
 def _build_arg_parser():
-    p = argparse.ArgumentParser(description=__doc__, epilog=EPILOG,
-                                formatter_class=argparse.RawTextHelpFormatter)
+    p = argparse.ArgumentParser(description=__doc__,
+                                formatter_class=argparse.RawTextHelpFormatter,
+                                epilog=version_string)
 
     p.add_argument('in_moving_surface',
                    help='Input surface (.vtk).')

scripts/scil_surface_convert.py

@@ -11,6 +11,11 @@
 > scil_surface_convert.py surf.vtk converted_surf.ply
 
 Formerly: scil_convert_surface.py
+-----------------------------------------------------------------
+Reference:
+[1] St-Onge, E., Daducci, A., Girard, G. and Descoteaux, M. 2018.
+    Surface-enhanced tractography (SET). NeuroImage.
+-----------------------------------------------------------------
 """
 import argparse
 import logging
@@ -26,17 +31,13 @@
                              add_verbose_arg,
                              assert_inputs_exist,
                              assert_outputs_exist)
-
-EPILOG = """
-References:
-[1] St-Onge, E., Daducci, A., Girard, G. and Descoteaux, M. 2018.
-    Surface-enhanced tractography (SET). NeuroImage.
-"""
+from scilpy.version import version_string
 
 
 def _build_arg_parser():
-    p = argparse.ArgumentParser(description=__doc__, epilog=EPILOG,
-                                formatter_class=argparse.RawTextHelpFormatter)
+    p = argparse.ArgumentParser(description=__doc__,
+                                formatter_class=argparse.RawTextHelpFormatter,
+                                epilog=version_string)
 
     p.add_argument('in_surface',
                    help='Input a surface (FreeSurfer or supported by VTK).')

scripts/scil_surface_create.py

@@ -10,6 +10,11 @@
 scil_surface_create.py out_surface.vtk \\
     --in_labels s1a1/mask/S1-A1_wmparc.a2009s.nii.gz\\
     --list_indices 16:32 --opening 2 --smooth 2 -v
+-----------------------------------------------------------------
+Reference:
+[1] St-Onge, E., Daducci, A., Girard, G. and Descoteaux, M. 2018.
+    Surface-enhanced tractography (SET). NeuroImage.
+-----------------------------------------------------------------
 """
 
 import argparse
@@ -35,17 +40,13 @@
                              assert_inputs_exist,
                              assert_outputs_exist,
                              ranged_type)
-
-EPILOG = """
-References:
-[1] St-Onge, E., Daducci, A., Girard, G. and Descoteaux, M. 2018.
-    Surface-enhanced tractography (SET). NeuroImage.
-"""
+from scilpy.version import version_string
 
 
 def _build_arg_parser():
-    p = argparse.ArgumentParser(description=__doc__, epilog=EPILOG,
-                                formatter_class=argparse.RawTextHelpFormatter)
+    p = argparse.ArgumentParser(description=__doc__,
+                                formatter_class=argparse.RawTextHelpFormatter,
+                                epilog=version_string)
 
     g1 = p.add_argument_group("Input (Labels or Mask)")
     mxg = g1.add_mutually_exclusive_group(required=True)