Add Scilpy version - part 1

scilpy/version.py

@@ -17,6 +17,7 @@
     _ver.append(_version_extra)
 
 __version__ = '.'.join(map(str, _ver))
+version_string = "\nScilpy version: " + __version__
 
 CLASSIFIERS = ["Development Status :: 3 - Alpha",
                "Environment :: Console",

scripts/scil_aodf_metrics.py

@@ -24,6 +24,22 @@
 SH coefficients.
 
 Formerly: scil_compute_asym_odf_metrics.py
+--------------------------------------------------------------------------------
+References:
+[1] C. Poirier and M. Descoteaux, "Filtering Methods for Asymmetric ODFs:
+    Where and How Asymmetry Occurs in the White Matter." bioRxiv. 2022 Jan 1;
+    2022.12.18.520881. doi: https://doi.org/10.1101/2022.12.18.520881
+
+[2] S. Cetin Karayumak, E. Özarslan, and G. Unal,"Asymmetric Orientation 
+    Distribution Functions (AODFs) revealing intravoxel geometry in diffusion MRI"
+    Magnetic Resonance Imaging, vol. 49, pp. 145-158, Jun. 2018,
+    doi: https://doi.org/10.1016/j.mri.2018.03.006.
+
+[3] C. Poirier, E. St-Onge, and M. Descoteaux, "Investigating the Occurence of
+    Asymmetric Patterns in White Matter Fiber Orientation Distribution Functions"
+    [Abstract], In: Proc. Intl. Soc. Mag. Reson. Med. 29 (2021), 2021 May 15-20,
+    Vancouver, BC, Abstract number 0865.
+---------------------------------------------------------------------------------
 """
 
 
@@ -44,29 +60,14 @@
                              assert_headers_compatible, assert_outputs_exist,
                              add_overwrite_arg, parse_sh_basis_arg)
 from scilpy.io.image import get_data_as_mask
-
-
-EPILOG = """
-References:
-[1] C. Poirier and M. Descoteaux, "Filtering Methods for Asymmetric ODFs:
-Where and How Asymmetry Occurs in the White Matter." bioRxiv. 2022 Jan 1;
-2022.12.18.520881. doi: https://doi.org/10.1101/2022.12.18.520881
-
-[2] S. Cetin Karayumak, E. Özarslan, and G. Unal,
-"Asymmetric Orientation Distribution Functions (AODFs) revealing intravoxel
-geometry in diffusion MRI," Magnetic Resonance Imaging, vol. 49, pp. 145-158,
-Jun. 2018, doi: https://doi.org/10.1016/j.mri.2018.03.006.
-
-[3] C. Poirier, E. St-Onge, and M. Descoteaux, "Investigating the Occurence of
-Asymmetric Patterns in White Matter Fiber Orientation Distribution Functions"
-[Abstract], In: Proc. Intl. Soc. Mag. Reson. Med. 29 (2021), 2021 May 15-20,
-Vancouver, BC, Abstract number 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='Input SH image.')
 
     p.add_argument('--mask',

scripts/scil_bids_validate.py

@@ -34,7 +34,7 @@
 from scilpy.io.utils import (add_overwrite_arg, add_verbose_arg,
                              assert_inputs_exist,
                              assert_outputs_exist)
-
+from scilpy.version import version_string
 
 conversion = {"i": "x",
               "i-": "x-",
@@ -49,9 +49,9 @@
 
 
 def _build_arg_parser():
-    p = argparse.ArgumentParser(
-        formatter_class=argparse.RawDescriptionHelpFormatter,
-        description=__doc__)
+    p = argparse.ArgumentParser(description=__doc__,
+                                formatter_class=argparse.RawTextHelpFormatter,
+                                epilog=version_string)
 
     p.add_argument("in_bids",
                    help="Input BIDS folder.")

scripts/scil_bingham_metrics.py

@@ -17,6 +17,18 @@
 with 1mm isotropic resolution. Other metrics take less than a second.
 
 Formerly: scil_compute_lobe_specific_fodf_metrics.py
+------------------------------------------------------------------------------
+References:
+[1] T. W. Riffert, J. Schreiber, A. Anwander, and T. R. Knösche, “Beyond
+    fractional anisotropy: Extraction of bundle-specific structural metrics
+    from crossing fiber models,” NeuroImage, vol. 100, pp. 176-191, Oct. 2014,
+    doi: 10.1016/j.neuroimage.2014.06.015.
+
+[2] J. Schreiber, T. Riffert, A. Anwander, and T. R. Knösche, “Plausibility
+    Tracking: A method to evaluate anatomical connectivity and microstructural
+    properties along fiber pathways,” NeuroImage, vol. 90, pp. 163-178, Apr.
+    2014, doi: 10.1016/j.neuroimage.2014.01.002.
+------------------------------------------------------------------------------
 """
 
 import nibabel as nib
@@ -33,24 +45,14 @@
                                     compute_fiber_spread,
                                     compute_fiber_fraction)
 
-
-EPILOG = """
-[1] T. W. Riffert, J. Schreiber, A. Anwander, and T. R. Knösche, “Beyond
-    fractional anisotropy: Extraction of bundle-specific structural metrics
-    from crossing fiber models,” NeuroImage, vol. 100, pp. 176-191, Oct. 2014,
-    doi: 10.1016/j.neuroimage.2014.06.015.
-
-[2] J. Schreiber, T. Riffert, A. Anwander, and T. R. Knösche, “Plausibility
-    Tracking: A method to evaluate anatomical connectivity and microstructural
-    properties along fiber pathways,” NeuroImage, vol. 90, pp. 163-178, Apr.
-    2014, doi: 10.1016/j.neuroimage.2014.01.002.
-"""
+from scilpy.version import version_string
 
 
 def _build_arg_parser():
     p = argparse.ArgumentParser(description=__doc__,
                                 formatter_class=argparse.RawTextHelpFormatter,
-                                epilog=EPILOG)
+                                epilog=version_string)
+
     p.add_argument('in_bingham',
                    help='Input Bingham nifti image.')
 

scripts/scil_btensor_metrics.py

@@ -54,11 +54,13 @@
                              add_verbose_arg, add_skip_b0_check_arg,
                              add_tolerance_arg, assert_headers_compatible)
 from scilpy.reconst.divide import fit_gamma, gamma_fit2metrics
+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_dwis', nargs='+', required=True,
                    help='Path to the input diffusion volume for each '

scripts/scil_bundle_alter_to_target_dice.py

@@ -52,11 +52,14 @@
 from scilpy.tractograms.tractogram_operations import transform_streamlines_alter, \
     trim_streamlines_alter, cut_streamlines_alter, subsample_streamlines_alter, \
     replace_streamlines_alter, shuffle_streamlines, shuffle_streamlines_orientation
+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_bundle',
                    help='Input bundle filename (.trk, .tck).')
     p.add_argument('out_bundle',

scripts/scil_bundle_clean_qbx_clusters.py

@@ -34,11 +34,13 @@
                              assert_outputs_exist,
                              assert_output_dirs_exist_and_empty,
                              assert_headers_compatible)
+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_bundles', nargs='+',
                    help='List of the clusters filename.')

scripts/scil_bundle_compute_centroid.py

@@ -20,12 +20,13 @@
                              add_verbose_arg,
                              add_reference_arg)
 from scilpy.tractanalysis.bundle_operations import get_streamlines_centroid
+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_bundle',
                    help='Fiber bundle file.')

scripts/scil_bundle_compute_endpoints_map.py

@@ -32,12 +32,13 @@
                              assert_outputs_exist)
 from scilpy.tractograms.streamline_and_mask_operations import \
     get_head_tail_density_maps
+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_bundle',
                    help='Fiber bundle filename.')

scripts/scil_bundle_diameter.py

@@ -53,11 +53,14 @@
 from scilpy.viz.backends.vtk import create_tube_with_radii
 from scilpy.viz.color import get_lookup_table
 from scilpy.viz.screenshot import compose_image
+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_bundles', nargs='+',
                    help='List of tractography files.')
     p.add_argument('in_labels', nargs='+',

scripts/scil_bundle_filter_by_occurence.py

@@ -31,11 +31,13 @@
 from scilpy.tractanalysis.streamlines_metrics import compute_tract_counts_map
 from scilpy.tractograms.tractogram_operations import (
     intersection_robust, union_robust)
+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_bundles', nargs='+',
                    help='Input bundles filename(s). All tractograms must have '

scripts/scil_bundle_fixel_analysis.py

@@ -106,11 +106,14 @@
                              add_verbose_arg,
                              assert_output_dirs_exist_and_empty)
 from scilpy.tractanalysis.fixel_density import (fixel_density, maps_to_masks)
+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_peaks',
                    help='Path of the peaks. The peaks are expected to be '
                         'given as unit directions. \nTo get these from fODF '

scripts/scil_bundle_generate_priors.py

@@ -7,6 +7,11 @@
 be used for bundle-specific tractography, but not for FOD metrics.
 
 Formerly: scil_generate_priors_from_bundle.py
+-----------------------------------------------------------------------------
+Reference:
+[1] Rheault, Francois, et al. "Bundle-specific tractography with incorporated
+    anatomical and orientational priors." NeuroImage 186 (2019): 382-398
+-----------------------------------------------------------------------------
 """
 
 import argparse
@@ -30,19 +35,14 @@
                              assert_headers_compatible)
 from scilpy.reconst.utils import find_order_from_nb_coeff
 from scilpy.tractanalysis.todi import TrackOrientationDensityImaging
-
-
-EPILOG = """
-    References:
-        [1] Rheault, Francois, et al. "Bundle-specific tractography with
-        incorporated anatomical and orientational priors."
-        NeuroImage 186 (2019): 382-398
-    """
+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_bundle',
                    help='Input bundle filename.')
 

scripts/scil_bundle_label_map.py

@@ -44,12 +44,13 @@
 from scilpy.tractograms.streamline_operations import \
     resample_streamlines_num_points
 from scilpy.viz.color import get_lookup_table
+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_bundles', nargs='+',
                    help='Fiber bundle file.')

scripts/scil_bundle_mean_fixel_afd.py

@@ -11,6 +11,14 @@
 Please use a bundle file rather than a whole tractogram.
 
 Formerly: scil_compute_fixel_afd_from_bundles.py
+-----------------------------------------------------------------------------
+Reference:
+[1] Raffelt, D., Tournier, JD., Rose, S., Ridgway, GR., Henderson, R.,
+    Crozier, S., Salvado, O., & Connelly, A. (2012).
+    Apparent Fibre Density: a novel measure for the analysis of
+    diffusion-weighted magnetic resonance images. NeuroImage, 59(4),
+    3976--3994.
+-----------------------------------------------------------------------------
 """
 
 import argparse
@@ -26,20 +34,14 @@
                              parse_sh_basis_arg, assert_headers_compatible)
 from scilpy.tractanalysis.afd_along_streamlines \
     import afd_map_along_streamlines
-
-EPILOG = """
-Reference:
-    [1] Raffelt, D., Tournier, JD., Rose, S., Ridgway, GR., Henderson, R.,
-        Crozier, S., Salvado, O., & Connelly, A. (2012).
-        Apparent Fibre Density: a novel measure for the analysis of
-        diffusion-weighted magnetic resonance images. NeuroImage, 59(4),
-        3976--3994.
-"""
+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_bundle',
                    help='Path of the bundle file.')
     p.add_argument('in_fodf',