From 2ff000221886e1fe30f661dac0e08615cbd835ed Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Thu, 16 Nov 2023 15:16:37 -0500
Subject: [PATCH 01/97] project maps to streamline points and do math

---
 scripts/scil_project_map_to_streamlines.py | 158 ++++++++++++
 scripts/scil_streamlines_point_math.py     | 286 +++++++++++++++++++++
 2 files changed, 444 insertions(+)
 create mode 100755 scripts/scil_project_map_to_streamlines.py
 create mode 100755 scripts/scil_streamlines_point_math.py

diff --git a/scripts/scil_project_map_to_streamlines.py b/scripts/scil_project_map_to_streamlines.py
new file mode 100755
index 000000000..be45a93b1
--- /dev/null
+++ b/scripts/scil_project_map_to_streamlines.py
@@ -0,0 +1,158 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+Projects metrics extracted from a map onto the endpoints of streamlines. 
+
+The default options will take data from a nifti image (3D or ND) and 
+project it onto the endpoints of streamlines.
+"""
+
+import argparse
+import logging
+from copy import deepcopy
+
+from numpy import asarray, reshape, repeat
+
+from scilpy.io.image import assert_same_resolution, load_img
+from scilpy.io.streamlines import load_tractogram_with_reference
+from scilpy.io.utils import (add_overwrite_arg,
+                             assert_inputs_exist,
+                             assert_outputs_exist,
+                             add_reference_arg,
+                             add_verbose_arg)
+
+from scilpy.image.volume_space_management import DataVolume
+
+from dipy.io.streamline import save_tractogram, StatefulTractogram
+
+def project_metric_to_streamlines(sft, metric, endpoints_only=False):
+    """
+    Projects a metric onto the points of streamlines.
+
+    Parameters
+    ----------
+    sft: StatefulTractogram
+        Input tractogram.
+    metric: DataVolume
+        Input metric.
+
+    Optional:
+    ---------
+    endpoints_only: bool
+        If True, will only project the metric onto the endpoints of the 
+        streamlines (all values along streamlines set to zero). If False, 
+        will project the metric onto all points of the streamlines.
+        
+    Returns
+    -------
+    streamline_data: 
+        metric projected to each point of the streamlines.
+    """
+    if len(metric.data.shape) == 4:
+        dimension = metric.data.shape[3]
+    else:
+        dimension = 1
+
+    streamline_data = []
+    if endpoints_only:
+        for s in sft.streamlines:
+            p1_data = metric.get_value_at_coordinate(s[0][0], s[0][1], s[0][2], space=sft.space, origin=sft.origin)
+            p2_data = metric.get_value_at_coordinate(s[-1][0], s[-1][1], s[-1][2], space=sft.space, origin=sft.origin)
+            thisstreamline_data = []
+            for p in s:
+                thisstreamline_data.append(asarray(repeat(0, p1_data.shape[0])))
+
+            thisstreamline_data[0] = p1_data
+            thisstreamline_data[-1] = p2_data
+            thisstreamline_data = asarray(thisstreamline_data)
+
+            streamline_data.append(reshape(thisstreamline_data, (len(thisstreamline_data), dimension)))
+    else:
+        for s in sft.streamlines:
+            thisstreamline_data = []
+            for p in s:
+                thisstreamline_data.append(metric.get_value_at_coordinate(p[0], p[1], p[2], space=sft.space, origin=sft.origin))
+
+            streamline_data.append(reshape(thisstreamline_data, (len(thisstreamline_data), dimension)))
+
+    return streamline_data
+    
+def _build_arg_parser():
+    p = argparse.ArgumentParser(
+        description=__doc__,
+        formatter_class=argparse.RawTextHelpFormatter)
+
+    # Mandatory arguments input and output tractogram must be in trk format
+    p.add_argument('in_tractogram', 
+                   help='Fiber bundle file.')
+    p.add_argument('in_metric',
+                   help='Nifti metric to project onto streamlines.')
+    p.add_argument('out_tractogram', 
+                   help='Output file.')
+
+    # Optional arguments
+    p.add_argument('--trilinear', action='store_true',
+                   help='If set, will use trilinear interpolation \n'
+                        'else will use nearest neighbor interpolation \n'
+                        'by default.')
+    
+    p.add_argument('--endpoints_only', action='store_true',
+                     help='If set, will only project the metric onto the endpoints \n'
+                            'of the streamlines (all other values along streamlines set to zero). \n'
+                            'If not set, will project the metric onto all points of the streamlines.')
+
+    p.add_argument('--dpp_name', default='metric',
+                   help='Name of the data_per_point to be saved in the output tractogram. \n'
+                        '(Default: %(default)s)')
+    add_reference_arg(p)
+    add_overwrite_arg(p)
+    add_verbose_arg(p)
+    return p
+
+
+def main():
+    parser = _build_arg_parser()
+    args = parser.parse_args()
+
+    assert_inputs_exist(parser, [args.in_tractogram, args.in_metric])
+    
+    assert_outputs_exist(parser, args, [args.out_tractogram])
+
+    logging.debug("Loading the tractogram...")
+    sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
+    sft.to_vox()
+    sft.to_corner()
+
+    if len(sft.streamlines) == 0:
+        logging.warning('Empty bundle file {}. Skipping'.format(args.bundle))
+        return
+    
+    logging.debug("Loading the metric...")
+    metric_img,metric_dtype = load_img(args.in_metric)
+    assert_same_resolution((args.in_tractogram, args.in_metric))
+    metric_data = metric_img.get_fdata(caching='unchanged', dtype=float)
+    metric_res = metric_img.header.get_zooms()[:3]
+    
+    if args.trilinear:
+        interp = "trilinear" 
+    else:
+        interp = "nearest"
+    
+    metric = DataVolume(metric_data, metric_res, interp)
+    
+    logging.debug("Projecting metric onto streamlines")
+    streamline_data = project_metric_to_streamlines(sft, metric, 
+                            endpoints_only=args.endpoints_only)
+
+    logging.debug("Saving the tractogram...")
+    data_per_point = {}
+    data_per_point[args.dpp_name] = streamline_data
+    out_sft = StatefulTractogram(sft.streamlines, metric_img,
+                                 sft.space, sft.origin, data_per_point=data_per_point)
+    save_tractogram(out_sft, args.out_tractogram)
+    print(out_sft.data_per_point[args.dpp_name][0][0])
+    print(out_sft.data_per_point[args.dpp_name][0][-1])
+
+if __name__ == '__main__':
+    main()
diff --git a/scripts/scil_streamlines_point_math.py b/scripts/scil_streamlines_point_math.py
new file mode 100755
index 000000000..b70cbe47f
--- /dev/null
+++ b/scripts/scil_streamlines_point_math.py
@@ -0,0 +1,286 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+Performs an operation on data per point from streamlines 
+resulting in data per streamline.  The supported
+operations are:
+
+If the input is singular per point then:
+mean: mean across points per streamline
+sum: sum across points per streamline
+min: min value across points per streamline
+max: max value across points per streamline
+
+endpoints_only is set, min/max/mean/sum will only 
+be calculated using the streamline endpoints
+
+If the input is multivalued per point then: 
+mean: mean calculated per point for each streamline
+sum: sum calculated per point for each streamline
+min: min value calculated per point for each streamline
+max: max value calculated per point for each streamline
+
+endpoints_only is set, min/max/mean/sum will only
+be calculated at the streamline endpoints
+
+Endpoint only operations:
+correlation: correlation calculated between arrays extracted from
+streamline endpoints (data must be multivalued per point)
+"""
+
+import argparse
+import logging
+
+from copy import deepcopy
+
+from dipy.io.streamline import save_tractogram, StatefulTractogram
+import numpy as np
+from numpy import asarray, reshape
+
+from scilpy.io.streamlines import load_tractogram_with_reference
+from scilpy.io.utils import (add_bbox_arg,
+                             add_overwrite_arg,
+                             add_reference_arg,
+                             add_verbose_arg,
+                             assert_inputs_exist,
+                             assert_outputs_exist)
+
+def perform_operation_per_point(op_name, sft, dpp_name='metric', endpoints_only=False):
+    """Peforms an operation per point for all streamlines.
+
+    Parameters
+    ----------
+    op_name: str
+        A callable that takes a list of streamline data per point (4D) and
+        returns a list of streamline data per point.
+    sft: StatefulTractogram
+        The streamlines used in the operation.
+    dpp_name: str
+        The name of the data per point to be used in the operation.
+    endpoints_only: bool
+        If True, will only perform operation on endpoints
+    
+    Returns
+    -------
+    new_sft: StatefulTractogram
+        sft with data per streamline resulting from the operation.
+    """
+    # Performing operation
+    call_op = OPERATIONS[op_name]
+    if endpoints_only:
+        new_data_per_point = []
+        for s in sft.data_per_point[dpp_name]:
+            this_data_per_point = []
+            for p in s:
+                this_data_per_point.append(asarray(0.))
+            this_data_per_point[0] = call_op(s[0])
+            this_data_per_point[-1] = call_op(s[-1])
+            new_data_per_point.append(reshape(this_data_per_point, (len(this_data_per_point), 1)))
+    else:
+        new_data_per_point = []
+        for s in sft.data_per_point[dpp_name]:
+            this_data_per_point = []
+            for p in s:
+                this_data_per_point.append(call_op(p))
+            new_data_per_point.append(reshape(this_data_per_point, (len(this_data_per_point), 1)))
+
+    # Extracting streamlines
+    return new_data_per_point
+
+def perform_operation_per_streamline(op_name, sft, dpp_name='metric', endpoints_only=False):
+    """Peforms an operation across points for each streamline.
+
+    Parameters
+    ----------
+    op_name: str
+        A callable that takes a list of streamline data per streamline and
+        returns a list of data per streamline.
+    sft: StatefulTractogram
+        The streamlines used in the operation.
+    dpp_name: str
+        The name of the data per point to be used in the operation.
+    endpoints_only: bool
+        If True, will only perform operation on endpoints
+    
+    Returns
+    -------
+    new_sft: StatefulTractogram
+        sft with data per streamline resulting from the operation.
+    """
+    # Performing operation
+    call_op = OPERATIONS[op_name]
+    if endpoints_only:
+        new_data_per_streamline = []
+        for s in sft.data_per_point[dpp_name]:
+            new_data_per_streamline.append(call_op([s[0], s[-1]]))
+    else:
+        new_data_per_streamline = []
+        for s in sft.data_per_point[dpp_name]:
+            new_data_per_streamline.append(call_op(s))
+
+    return new_data_per_streamline
+
+def perform_operation_across_endpoints(op_name, sft, dpp_name='metric'):
+    """Peforms an operation across endpoints for each streamline.
+
+    Parameters
+    ----------
+    op_name: str
+        A callable that takes a list of streamline data per streamline and
+        returns a list of data per streamline.
+    sft: StatefulTractogram
+        The streamlines used in the operation.
+    dpp_name: str
+        The name of the data per point to be used in the operation.
+    
+    Returns
+    -------
+    new_sft: StatefulTractogram
+        sft with data per streamline resulting from the operation.
+    """
+    # Performing operation
+    call_op = OPERATIONS[op_name]
+    new_data_per_streamline = []
+    for s in sft.data_per_point[dpp_name]:
+        new_data_per_streamline.append(call_op(s[0], s[-1])[0,1])
+
+    return new_data_per_streamline
+
+def mean(array):
+    return np.mean(array)
+
+def sum(array):
+    return np.sum(array)
+
+def min(array):
+    return np.min(array)
+
+def max(array):
+    return np.max(array)
+
+def correlation(array1, array2):
+    return np.corrcoef(array1, array2)
+
+OPERATIONS = {
+    'mean': mean,
+    'sum': sum,
+    'min': min,
+    'max': max,
+    'correlation': correlation,
+}
+
+def _build_arg_parser():
+    p = argparse.ArgumentParser(
+        formatter_class=argparse.RawTextHelpFormatter,
+        description=__doc__)
+
+    p.add_argument('operation', metavar='OPERATION',
+                   choices=['mean', 'sum', 'min',
+                            'max', 'correlation'],
+                   help='The type of operation to be performed on the '
+                        'streamlines. Must\nbe one of the following: '
+                        '%(choices)s.')
+    p.add_argument('in_tractogram', metavar='INPUT_FILE',
+                   help='Input tractogram containing streamlines and '
+                        'metadata.')
+    p.add_argument('out_tractogram', metavar='OUTPUT_FILE',
+                   help='The file where the remaining streamlines '
+                        'are saved.')
+    
+    p.add_argument('--endpoints_only', action='store_true', default=False,
+                        help='If set, will only perform operation on endpoints \n'
+                        'If not set, will perform operation on all streamline points.')
+    p.add_argument('--dpp_name', default='metric',
+                   help='Name of the data_per_point for operation to be '
+                        'performed on. (Default: %(default)s)')
+    
+    p.add_argument('--output_dpp_name', default='metric_math',
+                   help='Name of the resulting data_per_point to be saved in the output '
+                        'tractogram. (Default: %(default)s)')
+
+    add_reference_arg(p)
+    add_verbose_arg(p)
+    add_overwrite_arg(p)
+    add_bbox_arg(p)
+
+    return p
+
+def main():
+    parser = _build_arg_parser()
+    args = parser.parse_args()
+
+    if args.verbose:
+        logging.getLogger().setLevel(logging.INFO)
+
+    assert_inputs_exist(parser, args.in_tractogram)
+    assert_outputs_exist(parser, args, args.out_tractogram)
+
+    # Load the input files.
+    logging.info("Loading file {}".format(args.in_tractogram))
+    sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
+
+    if len(sft.streamlines) == 0:
+        logging.info("Input tractogram contains no streamlines. Exiting.")
+        return
+
+    # Check to see if the data per point exists.
+    if args.dpp_name not in sft.data_per_point:
+        logging.info('Data per point {} not found in input tractogram.'
+                         .format(args.dpp_name))
+        return
+    
+    # check size of first streamline data_per_point
+    if sft.data_per_point[args.dpp_name][0].shape[1] == 1:
+        is_singular = True
+    else:
+        is_singular = False
+
+    if args.operation == 'correlation' and is_singular:
+        logging.info('Correlation operation requires multivalued data per '
+                         'point. Exiting.')
+        return
+    
+    # Perform the requested operation.
+    if not is_singular:
+        if args.operation == 'correlation':
+            logging.info('Performing {}} across endpoint data')
+            new_data_per_streamline = perform_operation_across_endpoints(args.operation,sft, args.dpp_name)
+        
+            # Adding data per streamline to new_sft
+            new_sft = StatefulTractogram(sft.streamlines, sft.space_attributes,
+                                         sft.space, sft.origin,
+                                         data_per_streamline={args.output_dpp_name: new_data_per_streamline})
+        else:
+            # Results in new data per point
+            logging.info('Performing {} on data from each streamine point.'.format(args.operation))
+            new_data_per_point = perform_operation_per_point(
+                args.operation, sft, args.dpp_name, args.endpoints_only)
+
+            # Adding data per point to new_sft
+            new_sft = StatefulTractogram(sft.streamlines, sft.space_attributes,
+                                         sft.space, sft.origin,
+                                         data_per_point={args.output_dpp_name: new_data_per_point})
+    else:
+        # Results in new data per streamline
+        logging.info('Performing {} across each streamline.'.format(args.operation))
+        new_data_per_streamline = perform_operation_per_streamline(
+            args.operation, sft, args.output_dpp_name, args.endpoints_only)
+        
+        # Adding data per streamline to new_sft
+        new_sft = StatefulTractogram(sft.streamlines, sft.space_attributes,
+                                     sft.space, sft.origin,
+                                     data_per_streamline={args.dpp_name: new_data_per_streamline})
+
+    if len(new_sft) == 0 and not args.save_empty:
+        logging.info("Empty resulting tractogram. Not saving results.")
+        return
+
+    # Save the new streamlines (and metadata)
+    logging.info('Saving {} streamlines to {}.'.format(len(new_sft),
+                                                       args.out_tractogram))
+    save_tractogram(new_sft, args.out_tractogram,
+                    bbox_valid_check=args.bbox_check)
+
+if __name__ == "__main__":
+    main()

From 7eef429d0f9da20e226c1a3354bffc765c81ea14 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Thu, 23 Nov 2023 13:34:49 -0500
Subject: [PATCH 02/97] fixed pep8

---
 scripts/scil_project_map_to_streamlines.py | 55 +++++++++++++---------
 scripts/scil_streamlines_point_math.py     | 55 ++++++++++++++--------
 2 files changed, 68 insertions(+), 42 deletions(-)

diff --git a/scripts/scil_project_map_to_streamlines.py b/scripts/scil_project_map_to_streamlines.py
index be45a93b1..c9f0497d5 100755
--- a/scripts/scil_project_map_to_streamlines.py
+++ b/scripts/scil_project_map_to_streamlines.py
@@ -26,6 +26,7 @@
 
 from dipy.io.streamline import save_tractogram, StatefulTractogram
 
+
 def project_metric_to_streamlines(sft, metric, endpoints_only=False):
     """
     Projects a metric onto the points of streamlines.
@@ -43,7 +44,7 @@ def project_metric_to_streamlines(sft, metric, endpoints_only=False):
         If True, will only project the metric onto the endpoints of the 
         streamlines (all values along streamlines set to zero). If False, 
         will project the metric onto all points of the streamlines.
-        
+
     Returns
     -------
     streamline_data: 
@@ -57,38 +58,45 @@ def project_metric_to_streamlines(sft, metric, endpoints_only=False):
     streamline_data = []
     if endpoints_only:
         for s in sft.streamlines:
-            p1_data = metric.get_value_at_coordinate(s[0][0], s[0][1], s[0][2], space=sft.space, origin=sft.origin)
-            p2_data = metric.get_value_at_coordinate(s[-1][0], s[-1][1], s[-1][2], space=sft.space, origin=sft.origin)
+            p1_data = metric.get_value_at_coordinate(
+                s[0][0], s[0][1], s[0][2], space=sft.space, origin=sft.origin)
+            p2_data = metric.get_value_at_coordinate(
+                s[-1][0], s[-1][1], s[-1][2], space=sft.space, origin=sft.origin)
             thisstreamline_data = []
             for p in s:
-                thisstreamline_data.append(asarray(repeat(0, p1_data.shape[0])))
+                thisstreamline_data.append(
+                    asarray(repeat(0, p1_data.shape[0])))
 
             thisstreamline_data[0] = p1_data
             thisstreamline_data[-1] = p2_data
             thisstreamline_data = asarray(thisstreamline_data)
 
-            streamline_data.append(reshape(thisstreamline_data, (len(thisstreamline_data), dimension)))
+            streamline_data.append(
+                reshape(thisstreamline_data, (len(thisstreamline_data), dimension)))
     else:
         for s in sft.streamlines:
             thisstreamline_data = []
             for p in s:
-                thisstreamline_data.append(metric.get_value_at_coordinate(p[0], p[1], p[2], space=sft.space, origin=sft.origin))
+                thisstreamline_data.append(metric.get_value_at_coordinate(
+                    p[0], p[1], p[2], space=sft.space, origin=sft.origin))
 
-            streamline_data.append(reshape(thisstreamline_data, (len(thisstreamline_data), dimension)))
+            streamline_data.append(
+                reshape(thisstreamline_data, (len(thisstreamline_data), dimension)))
 
     return streamline_data
-    
+
+
 def _build_arg_parser():
     p = argparse.ArgumentParser(
         description=__doc__,
         formatter_class=argparse.RawTextHelpFormatter)
 
     # Mandatory arguments input and output tractogram must be in trk format
-    p.add_argument('in_tractogram', 
+    p.add_argument('in_tractogram',
                    help='Fiber bundle file.')
     p.add_argument('in_metric',
                    help='Nifti metric to project onto streamlines.')
-    p.add_argument('out_tractogram', 
+    p.add_argument('out_tractogram',
                    help='Output file.')
 
     # Optional arguments
@@ -96,11 +104,11 @@ def _build_arg_parser():
                    help='If set, will use trilinear interpolation \n'
                         'else will use nearest neighbor interpolation \n'
                         'by default.')
-    
+
     p.add_argument('--endpoints_only', action='store_true',
-                     help='If set, will only project the metric onto the endpoints \n'
-                            'of the streamlines (all other values along streamlines set to zero). \n'
-                            'If not set, will project the metric onto all points of the streamlines.')
+                   help='If set, will only project the metric onto the endpoints \n'
+                   'of the streamlines (all other values along streamlines set to zero). \n'
+                   'If not set, will project the metric onto all points of the streamlines.')
 
     p.add_argument('--dpp_name', default='metric',
                    help='Name of the data_per_point to be saved in the output tractogram. \n'
@@ -116,7 +124,7 @@ def main():
     args = parser.parse_args()
 
     assert_inputs_exist(parser, [args.in_tractogram, args.in_metric])
-    
+
     assert_outputs_exist(parser, args, [args.out_tractogram])
 
     logging.debug("Loading the tractogram...")
@@ -127,23 +135,23 @@ def main():
     if len(sft.streamlines) == 0:
         logging.warning('Empty bundle file {}. Skipping'.format(args.bundle))
         return
-    
+
     logging.debug("Loading the metric...")
-    metric_img,metric_dtype = load_img(args.in_metric)
+    metric_img, metric_dtype = load_img(args.in_metric)
     assert_same_resolution((args.in_tractogram, args.in_metric))
     metric_data = metric_img.get_fdata(caching='unchanged', dtype=float)
     metric_res = metric_img.header.get_zooms()[:3]
-    
+
     if args.trilinear:
-        interp = "trilinear" 
+        interp = "trilinear"
     else:
         interp = "nearest"
-    
+
     metric = DataVolume(metric_data, metric_res, interp)
-    
+
     logging.debug("Projecting metric onto streamlines")
-    streamline_data = project_metric_to_streamlines(sft, metric, 
-                            endpoints_only=args.endpoints_only)
+    streamline_data = project_metric_to_streamlines(sft, metric,
+                                                    endpoints_only=args.endpoints_only)
 
     logging.debug("Saving the tractogram...")
     data_per_point = {}
@@ -154,5 +162,6 @@ def main():
     print(out_sft.data_per_point[args.dpp_name][0][0])
     print(out_sft.data_per_point[args.dpp_name][0][-1])
 
+
 if __name__ == '__main__':
     main()
diff --git a/scripts/scil_streamlines_point_math.py b/scripts/scil_streamlines_point_math.py
index b70cbe47f..d3e30446d 100755
--- a/scripts/scil_streamlines_point_math.py
+++ b/scripts/scil_streamlines_point_math.py
@@ -46,6 +46,7 @@
                              assert_inputs_exist,
                              assert_outputs_exist)
 
+
 def perform_operation_per_point(op_name, sft, dpp_name='metric', endpoints_only=False):
     """Peforms an operation per point for all streamlines.
 
@@ -60,7 +61,7 @@ def perform_operation_per_point(op_name, sft, dpp_name='metric', endpoints_only=
         The name of the data per point to be used in the operation.
     endpoints_only: bool
         If True, will only perform operation on endpoints
-    
+
     Returns
     -------
     new_sft: StatefulTractogram
@@ -76,18 +77,21 @@ def perform_operation_per_point(op_name, sft, dpp_name='metric', endpoints_only=
                 this_data_per_point.append(asarray(0.))
             this_data_per_point[0] = call_op(s[0])
             this_data_per_point[-1] = call_op(s[-1])
-            new_data_per_point.append(reshape(this_data_per_point, (len(this_data_per_point), 1)))
+            new_data_per_point.append(
+                reshape(this_data_per_point, (len(this_data_per_point), 1)))
     else:
         new_data_per_point = []
         for s in sft.data_per_point[dpp_name]:
             this_data_per_point = []
             for p in s:
                 this_data_per_point.append(call_op(p))
-            new_data_per_point.append(reshape(this_data_per_point, (len(this_data_per_point), 1)))
+            new_data_per_point.append(
+                reshape(this_data_per_point, (len(this_data_per_point), 1)))
 
     # Extracting streamlines
     return new_data_per_point
 
+
 def perform_operation_per_streamline(op_name, sft, dpp_name='metric', endpoints_only=False):
     """Peforms an operation across points for each streamline.
 
@@ -102,7 +106,7 @@ def perform_operation_per_streamline(op_name, sft, dpp_name='metric', endpoints_
         The name of the data per point to be used in the operation.
     endpoints_only: bool
         If True, will only perform operation on endpoints
-    
+
     Returns
     -------
     new_sft: StatefulTractogram
@@ -121,6 +125,7 @@ def perform_operation_per_streamline(op_name, sft, dpp_name='metric', endpoints_
 
     return new_data_per_streamline
 
+
 def perform_operation_across_endpoints(op_name, sft, dpp_name='metric'):
     """Peforms an operation across endpoints for each streamline.
 
@@ -133,7 +138,7 @@ def perform_operation_across_endpoints(op_name, sft, dpp_name='metric'):
         The streamlines used in the operation.
     dpp_name: str
         The name of the data per point to be used in the operation.
-    
+
     Returns
     -------
     new_sft: StatefulTractogram
@@ -143,25 +148,31 @@ def perform_operation_across_endpoints(op_name, sft, dpp_name='metric'):
     call_op = OPERATIONS[op_name]
     new_data_per_streamline = []
     for s in sft.data_per_point[dpp_name]:
-        new_data_per_streamline.append(call_op(s[0], s[-1])[0,1])
+        new_data_per_streamline.append(call_op(s[0], s[-1])[0, 1])
 
     return new_data_per_streamline
 
+
 def mean(array):
     return np.mean(array)
 
+
 def sum(array):
     return np.sum(array)
 
+
 def min(array):
     return np.min(array)
 
+
 def max(array):
     return np.max(array)
 
+
 def correlation(array1, array2):
     return np.corrcoef(array1, array2)
 
+
 OPERATIONS = {
     'mean': mean,
     'sum': sum,
@@ -170,6 +181,7 @@ def correlation(array1, array2):
     'correlation': correlation,
 }
 
+
 def _build_arg_parser():
     p = argparse.ArgumentParser(
         formatter_class=argparse.RawTextHelpFormatter,
@@ -187,14 +199,14 @@ def _build_arg_parser():
     p.add_argument('out_tractogram', metavar='OUTPUT_FILE',
                    help='The file where the remaining streamlines '
                         'are saved.')
-    
+
     p.add_argument('--endpoints_only', action='store_true', default=False,
-                        help='If set, will only perform operation on endpoints \n'
-                        'If not set, will perform operation on all streamline points.')
+                   help='If set, will only perform operation on endpoints \n'
+                   'If not set, will perform operation on all streamline points.')
     p.add_argument('--dpp_name', default='metric',
                    help='Name of the data_per_point for operation to be '
                         'performed on. (Default: %(default)s)')
-    
+
     p.add_argument('--output_dpp_name', default='metric_math',
                    help='Name of the resulting data_per_point to be saved in the output '
                         'tractogram. (Default: %(default)s)')
@@ -206,6 +218,7 @@ def _build_arg_parser():
 
     return p
 
+
 def main():
     parser = _build_arg_parser()
     args = parser.parse_args()
@@ -227,9 +240,9 @@ def main():
     # Check to see if the data per point exists.
     if args.dpp_name not in sft.data_per_point:
         logging.info('Data per point {} not found in input tractogram.'
-                         .format(args.dpp_name))
+                     .format(args.dpp_name))
         return
-    
+
     # check size of first streamline data_per_point
     if sft.data_per_point[args.dpp_name][0].shape[1] == 1:
         is_singular = True
@@ -238,22 +251,24 @@ def main():
 
     if args.operation == 'correlation' and is_singular:
         logging.info('Correlation operation requires multivalued data per '
-                         'point. Exiting.')
+                     'point. Exiting.')
         return
-    
+
     # Perform the requested operation.
     if not is_singular:
         if args.operation == 'correlation':
             logging.info('Performing {}} across endpoint data')
-            new_data_per_streamline = perform_operation_across_endpoints(args.operation,sft, args.dpp_name)
-        
+            new_data_per_streamline = perform_operation_across_endpoints(
+                args.operation, sft, args.dpp_name)
+
             # Adding data per streamline to new_sft
             new_sft = StatefulTractogram(sft.streamlines, sft.space_attributes,
                                          sft.space, sft.origin,
                                          data_per_streamline={args.output_dpp_name: new_data_per_streamline})
         else:
             # Results in new data per point
-            logging.info('Performing {} on data from each streamine point.'.format(args.operation))
+            logging.info(
+                'Performing {} on data from each streamine point.'.format(args.operation))
             new_data_per_point = perform_operation_per_point(
                 args.operation, sft, args.dpp_name, args.endpoints_only)
 
@@ -263,10 +278,11 @@ def main():
                                          data_per_point={args.output_dpp_name: new_data_per_point})
     else:
         # Results in new data per streamline
-        logging.info('Performing {} across each streamline.'.format(args.operation))
+        logging.info(
+            'Performing {} across each streamline.'.format(args.operation))
         new_data_per_streamline = perform_operation_per_streamline(
             args.operation, sft, args.output_dpp_name, args.endpoints_only)
-        
+
         # Adding data per streamline to new_sft
         new_sft = StatefulTractogram(sft.streamlines, sft.space_attributes,
                                      sft.space, sft.origin,
@@ -282,5 +298,6 @@ def main():
     save_tractogram(new_sft, args.out_tractogram,
                     bbox_valid_check=args.bbox_check)
 
+
 if __name__ == "__main__":
     main()

From 4d64eb6f74b8f8ddc7a2730e14879b701d900f90 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Thu, 23 Nov 2023 13:36:18 -0500
Subject: [PATCH 03/97] fixed logging line

---
 scripts/scil_streamlines_point_math.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/scil_streamlines_point_math.py b/scripts/scil_streamlines_point_math.py
index d3e30446d..52bab6c8a 100755
--- a/scripts/scil_streamlines_point_math.py
+++ b/scripts/scil_streamlines_point_math.py
@@ -257,7 +257,7 @@ def main():
     # Perform the requested operation.
     if not is_singular:
         if args.operation == 'correlation':
-            logging.info('Performing {}} across endpoint data')
+            logging.info('Performing {} across endpoint data.'.format(args.operation))
             new_data_per_streamline = perform_operation_across_endpoints(
                 args.operation, sft, args.dpp_name)
 

From 2fb63cd2f16c93c3ef0564ad27844b74b47d9e86 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Thu, 23 Nov 2023 13:49:59 -0500
Subject: [PATCH 04/97] fixed trailing whitespace

---
 scripts/scil_project_map_to_streamlines.py | 10 +++++-----
 scripts/scil_streamlines_point_math.py     |  6 +++---
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/scripts/scil_project_map_to_streamlines.py b/scripts/scil_project_map_to_streamlines.py
index c9f0497d5..59a9588bd 100755
--- a/scripts/scil_project_map_to_streamlines.py
+++ b/scripts/scil_project_map_to_streamlines.py
@@ -2,9 +2,9 @@
 # -*- coding: utf-8 -*-
 
 """
-Projects metrics extracted from a map onto the endpoints of streamlines. 
+Projects metrics extracted from a map onto the endpoints of streamlines.
 
-The default options will take data from a nifti image (3D or ND) and 
+The default options will take data from a nifti image (3D or ND) and
 project it onto the endpoints of streamlines.
 """
 
@@ -41,13 +41,13 @@ def project_metric_to_streamlines(sft, metric, endpoints_only=False):
     Optional:
     ---------
     endpoints_only: bool
-        If True, will only project the metric onto the endpoints of the 
-        streamlines (all values along streamlines set to zero). If False, 
+        If True, will only project the metric onto the endpoints of the
+        streamlines (all values along streamlines set to zero). If False,
         will project the metric onto all points of the streamlines.
 
     Returns
     -------
-    streamline_data: 
+    streamline_data:
         metric projected to each point of the streamlines.
     """
     if len(metric.data.shape) == 4:
diff --git a/scripts/scil_streamlines_point_math.py b/scripts/scil_streamlines_point_math.py
index 52bab6c8a..a1487d733 100755
--- a/scripts/scil_streamlines_point_math.py
+++ b/scripts/scil_streamlines_point_math.py
@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 
 """
-Performs an operation on data per point from streamlines 
+Performs an operation on data per point from streamlines
 resulting in data per streamline.  The supported
 operations are:
 
@@ -12,10 +12,10 @@
 min: min value across points per streamline
 max: max value across points per streamline
 
-endpoints_only is set, min/max/mean/sum will only 
+endpoints_only is set, min/max/mean/sum will only
 be calculated using the streamline endpoints
 
-If the input is multivalued per point then: 
+If the input is multivalued per point then:
 mean: mean calculated per point for each streamline
 sum: sum calculated per point for each streamline
 min: min value calculated per point for each streamline

From ba5a516387654475b2df9edfd154677acc9131a8 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Thu, 23 Nov 2023 14:21:07 -0500
Subject: [PATCH 05/97] removed print statements

---
 scripts/scil_project_map_to_streamlines.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/scripts/scil_project_map_to_streamlines.py b/scripts/scil_project_map_to_streamlines.py
index 59a9588bd..1e05cdad3 100755
--- a/scripts/scil_project_map_to_streamlines.py
+++ b/scripts/scil_project_map_to_streamlines.py
@@ -159,8 +159,6 @@ def main():
     out_sft = StatefulTractogram(sft.streamlines, metric_img,
                                  sft.space, sft.origin, data_per_point=data_per_point)
     save_tractogram(out_sft, args.out_tractogram)
-    print(out_sft.data_per_point[args.dpp_name][0][0])
-    print(out_sft.data_per_point[args.dpp_name][0][-1])
 
 
 if __name__ == '__main__':

From 797bd95451954e0ca96201c5d3ff3f2d9e2ee0f2 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Thu, 23 Nov 2023 14:37:24 -0500
Subject: [PATCH 06/97] removed useless assert resolution

---
 scripts/scil_project_map_to_streamlines.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/scripts/scil_project_map_to_streamlines.py b/scripts/scil_project_map_to_streamlines.py
index 1e05cdad3..ddc22358f 100755
--- a/scripts/scil_project_map_to_streamlines.py
+++ b/scripts/scil_project_map_to_streamlines.py
@@ -14,7 +14,7 @@
 
 from numpy import asarray, reshape, repeat
 
-from scilpy.io.image import assert_same_resolution, load_img
+from scilpy.io.image import load_img
 from scilpy.io.streamlines import load_tractogram_with_reference
 from scilpy.io.utils import (add_overwrite_arg,
                              assert_inputs_exist,
@@ -138,7 +138,6 @@ def main():
 
     logging.debug("Loading the metric...")
     metric_img, metric_dtype = load_img(args.in_metric)
-    assert_same_resolution((args.in_tractogram, args.in_metric))
     metric_data = metric_img.get_fdata(caching='unchanged', dtype=float)
     metric_res = metric_img.header.get_zooms()[:3]
 

From cf12dc7bcc8f4a5d5d06a2181d000686adc3cca1 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Fri, 24 Nov 2023 09:55:30 -0500
Subject: [PATCH 07/97] changed to voxel world coords for interpolation

---
 scripts/scil_project_map_to_streamlines.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/scil_project_map_to_streamlines.py b/scripts/scil_project_map_to_streamlines.py
index ddc22358f..2ef109064 100755
--- a/scripts/scil_project_map_to_streamlines.py
+++ b/scripts/scil_project_map_to_streamlines.py
@@ -129,7 +129,7 @@ def main():
 
     logging.debug("Loading the tractogram...")
     sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
-    sft.to_vox()
+    sft.to_voxmm()
     sft.to_corner()
 
     if len(sft.streamlines) == 0:

From 5d014a82b6b9cccb204e2d86328a7e95cdc0ee58 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Fri, 24 Nov 2023 10:57:14 -0500
Subject: [PATCH 08/97] fixed dimension error on endpoints only single val

---
 scripts/scil_project_map_to_streamlines.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/scripts/scil_project_map_to_streamlines.py b/scripts/scil_project_map_to_streamlines.py
index 2ef109064..bbb64acf1 100755
--- a/scripts/scil_project_map_to_streamlines.py
+++ b/scripts/scil_project_map_to_streamlines.py
@@ -64,8 +64,11 @@ def project_metric_to_streamlines(sft, metric, endpoints_only=False):
                 s[-1][0], s[-1][1], s[-1][2], space=sft.space, origin=sft.origin)
             thisstreamline_data = []
             for p in s:
-                thisstreamline_data.append(
-                    asarray(repeat(0, p1_data.shape[0])))
+                if dimension == 1:
+                    thisstreamline_data.append(0)
+                else:
+                    thisstreamline_data.append(
+                        asarray(repeat(0, p1_data.shape[0])))
 
             thisstreamline_data[0] = p1_data
             thisstreamline_data[-1] = p2_data

From 6de542cf5726faa8efd2c177ac4d935c1e03c6b4 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Fri, 24 Nov 2023 10:58:07 -0500
Subject: [PATCH 09/97] remove deepcopy

---
 scripts/scil_project_map_to_streamlines.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/scripts/scil_project_map_to_streamlines.py b/scripts/scil_project_map_to_streamlines.py
index bbb64acf1..e1764599d 100755
--- a/scripts/scil_project_map_to_streamlines.py
+++ b/scripts/scil_project_map_to_streamlines.py
@@ -10,7 +10,6 @@
 
 import argparse
 import logging
-from copy import deepcopy
 
 from numpy import asarray, reshape, repeat
 

From ba839fb5cdacb6a1714fa58387d9d3f01ec17f3e Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Fri, 24 Nov 2023 11:09:40 -0500
Subject: [PATCH 10/97] fixed too long lines

---
 scripts/scil_project_map_to_streamlines.py | 28 +++++++++-------
 scripts/scil_streamlines_point_math.py     | 37 +++++++++++++++-------
 2 files changed, 42 insertions(+), 23 deletions(-)

diff --git a/scripts/scil_project_map_to_streamlines.py b/scripts/scil_project_map_to_streamlines.py
index e1764599d..fe4a05c3a 100755
--- a/scripts/scil_project_map_to_streamlines.py
+++ b/scripts/scil_project_map_to_streamlines.py
@@ -58,9 +58,11 @@ def project_metric_to_streamlines(sft, metric, endpoints_only=False):
     if endpoints_only:
         for s in sft.streamlines:
             p1_data = metric.get_value_at_coordinate(
-                s[0][0], s[0][1], s[0][2], space=sft.space, origin=sft.origin)
+                s[0][0], s[0][1], s[0][2],
+                space=sft.space, origin=sft.origin)
             p2_data = metric.get_value_at_coordinate(
-                s[-1][0], s[-1][1], s[-1][2], space=sft.space, origin=sft.origin)
+                s[-1][0], s[-1][1], s[-1][2],
+                space=sft.space, origin=sft.origin)
             thisstreamline_data = []
             for p in s:
                 if dimension == 1:
@@ -74,7 +76,8 @@ def project_metric_to_streamlines(sft, metric, endpoints_only=False):
             thisstreamline_data = asarray(thisstreamline_data)
 
             streamline_data.append(
-                reshape(thisstreamline_data, (len(thisstreamline_data), dimension)))
+                reshape(thisstreamline_data,
+                        (len(thisstreamline_data), dimension)))
     else:
         for s in sft.streamlines:
             thisstreamline_data = []
@@ -83,7 +86,8 @@ def project_metric_to_streamlines(sft, metric, endpoints_only=False):
                     p[0], p[1], p[2], space=sft.space, origin=sft.origin))
 
             streamline_data.append(
-                reshape(thisstreamline_data, (len(thisstreamline_data), dimension)))
+                reshape(thisstreamline_data,
+                        (len(thisstreamline_data), dimension)))
 
     return streamline_data
 
@@ -108,13 +112,14 @@ def _build_arg_parser():
                         'by default.')
 
     p.add_argument('--endpoints_only', action='store_true',
-                   help='If set, will only project the metric onto the endpoints \n'
-                   'of the streamlines (all other values along streamlines set to zero). \n'
-                   'If not set, will project the metric onto all points of the streamlines.')
+                   help='If set, will only project the metric onto the \n'
+                   'endpoints of the streamlines (all other values along \n'
+                   ' streamlines set to zero). If not set, will project \n'
+                   ' the metric onto all points of the streamlines.')
 
     p.add_argument('--dpp_name', default='metric',
-                   help='Name of the data_per_point to be saved in the output tractogram. \n'
-                        '(Default: %(default)s)')
+                   help='Name of the data_per_point to be saved in the \n'
+                   'output tractogram. (Default: %(default)s)')
     add_reference_arg(p)
     add_overwrite_arg(p)
     add_verbose_arg(p)
@@ -152,13 +157,14 @@ def main():
 
     logging.debug("Projecting metric onto streamlines")
     streamline_data = project_metric_to_streamlines(sft, metric,
-                                                    endpoints_only=args.endpoints_only)
+                        endpoints_only=args.endpoints_only)
 
     logging.debug("Saving the tractogram...")
     data_per_point = {}
     data_per_point[args.dpp_name] = streamline_data
     out_sft = StatefulTractogram(sft.streamlines, metric_img,
-                                 sft.space, sft.origin, data_per_point=data_per_point)
+                                 sft.space, sft.origin,
+                                 data_per_point=data_per_point)
     save_tractogram(out_sft, args.out_tractogram)
 
 
diff --git a/scripts/scil_streamlines_point_math.py b/scripts/scil_streamlines_point_math.py
index a1487d733..2b42ea0ea 100755
--- a/scripts/scil_streamlines_point_math.py
+++ b/scripts/scil_streamlines_point_math.py
@@ -47,7 +47,8 @@
                              assert_outputs_exist)
 
 
-def perform_operation_per_point(op_name, sft, dpp_name='metric', endpoints_only=False):
+def perform_operation_per_point(op_name, sft, dpp_name='metric',
+                                endpoints_only=False):
     """Peforms an operation per point for all streamlines.
 
     Parameters
@@ -92,7 +93,8 @@ def perform_operation_per_point(op_name, sft, dpp_name='metric', endpoints_only=
     return new_data_per_point
 
 
-def perform_operation_per_streamline(op_name, sft, dpp_name='metric', endpoints_only=False):
+def perform_operation_per_streamline(op_name, sft, dpp_name='metric',
+                                     endpoints_only=False):
     """Peforms an operation across points for each streamline.
 
     Parameters
@@ -202,14 +204,15 @@ def _build_arg_parser():
 
     p.add_argument('--endpoints_only', action='store_true', default=False,
                    help='If set, will only perform operation on endpoints \n'
-                   'If not set, will perform operation on all streamline points.')
+                   'If not set, will perform operation on all streamline \n'
+                   'points.')
     p.add_argument('--dpp_name', default='metric',
                    help='Name of the data_per_point for operation to be '
                         'performed on. (Default: %(default)s)')
 
     p.add_argument('--output_dpp_name', default='metric_math',
-                   help='Name of the resulting data_per_point to be saved in the output '
-                        'tractogram. (Default: %(default)s)')
+                   help='Name of the resulting data_per_point to be saved \n'
+                   'in the output tractogram. (Default: %(default)s)')
 
     add_reference_arg(p)
     add_verbose_arg(p)
@@ -257,25 +260,33 @@ def main():
     # Perform the requested operation.
     if not is_singular:
         if args.operation == 'correlation':
-            logging.info('Performing {} across endpoint data.'.format(args.operation))
+            logging.info('Performing {} across endpoint data.'.format(
+                args.operation))
             new_data_per_streamline = perform_operation_across_endpoints(
                 args.operation, sft, args.dpp_name)
 
             # Adding data per streamline to new_sft
-            new_sft = StatefulTractogram(sft.streamlines, sft.space_attributes,
+            new_sft = StatefulTractogram(sft.streamlines,
+                                         sft.space_attributes,
                                          sft.space, sft.origin,
-                                         data_per_streamline={args.output_dpp_name: new_data_per_streamline})
+                                         data_per_streamline={
+                                             args.output_dpp_name:
+                                             new_data_per_streamline})
         else:
             # Results in new data per point
             logging.info(
-                'Performing {} on data from each streamine point.'.format(args.operation))
+                'Performing {} on data from each streamine point.'.format(
+                    args.operation))
             new_data_per_point = perform_operation_per_point(
                 args.operation, sft, args.dpp_name, args.endpoints_only)
 
             # Adding data per point to new_sft
-            new_sft = StatefulTractogram(sft.streamlines, sft.space_attributes,
+            new_sft = StatefulTractogram(sft.streamlines,
+                                         sft.space_attributes,
                                          sft.space, sft.origin,
-                                         data_per_point={args.output_dpp_name: new_data_per_point})
+                                         data_per_point={
+                                             args.output_dpp_name:
+                                             new_data_per_point})
     else:
         # Results in new data per streamline
         logging.info(
@@ -286,7 +297,9 @@ def main():
         # Adding data per streamline to new_sft
         new_sft = StatefulTractogram(sft.streamlines, sft.space_attributes,
                                      sft.space, sft.origin,
-                                     data_per_streamline={args.dpp_name: new_data_per_streamline})
+                                     data_per_streamline={
+                                         args.dpp_name:
+                                         new_data_per_streamline})
 
     if len(new_sft) == 0 and not args.save_empty:
         logging.info("Empty resulting tractogram. Not saving results.")

From a4af4acf6c2a741621fed66c8c0e48b9b080ca8a Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Fri, 24 Nov 2023 11:11:14 -0500
Subject: [PATCH 11/97] fixed indent

---
 scripts/scil_project_map_to_streamlines.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/scil_project_map_to_streamlines.py b/scripts/scil_project_map_to_streamlines.py
index fe4a05c3a..04e08fc43 100755
--- a/scripts/scil_project_map_to_streamlines.py
+++ b/scripts/scil_project_map_to_streamlines.py
@@ -157,7 +157,8 @@ def main():
 
     logging.debug("Projecting metric onto streamlines")
     streamline_data = project_metric_to_streamlines(sft, metric,
-                        endpoints_only=args.endpoints_only)
+                                                    endpoints_only=
+                                                    args.endpoints_only)
 
     logging.debug("Saving the tractogram...")
     data_per_point = {}

From fb0d9afe206c35993f1ec20b9531bd0424f2c6bf Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Fri, 24 Nov 2023 11:16:35 -0500
Subject: [PATCH 12/97] fixexed indents

---
 scripts/scil_project_map_to_streamlines.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/scripts/scil_project_map_to_streamlines.py b/scripts/scil_project_map_to_streamlines.py
index 04e08fc43..818700f84 100755
--- a/scripts/scil_project_map_to_streamlines.py
+++ b/scripts/scil_project_map_to_streamlines.py
@@ -156,9 +156,9 @@ def main():
     metric = DataVolume(metric_data, metric_res, interp)
 
     logging.debug("Projecting metric onto streamlines")
-    streamline_data = project_metric_to_streamlines(sft, metric,
-                                                    endpoints_only=
-                                                    args.endpoints_only)
+    streamline_data = project_metric_to_streamlines(
+        sft, metric,
+        endpoints_only=args.endpoints_only)
 
     logging.debug("Saving the tractogram...")
     data_per_point = {}

From 76a78c44fea7f89435e3522277e852d4ebd20a47 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Wed, 29 Nov 2023 14:13:55 -0500
Subject: [PATCH 13/97] update output dpp name

---
 scripts/scil_streamlines_point_math.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/scil_streamlines_point_math.py b/scripts/scil_streamlines_point_math.py
index 2b42ea0ea..5bbad7deb 100755
--- a/scripts/scil_streamlines_point_math.py
+++ b/scripts/scil_streamlines_point_math.py
@@ -292,13 +292,13 @@ def main():
         logging.info(
             'Performing {} across each streamline.'.format(args.operation))
         new_data_per_streamline = perform_operation_per_streamline(
-            args.operation, sft, args.output_dpp_name, args.endpoints_only)
+            args.operation, sft, args.dpp_name, args.endpoints_only)
 
         # Adding data per streamline to new_sft
         new_sft = StatefulTractogram(sft.streamlines, sft.space_attributes,
                                      sft.space, sft.origin,
                                      data_per_streamline={
-                                         args.dpp_name:
+                                         args.output_dpp_name:
                                          new_data_per_streamline})
 
     if len(new_sft) == 0 and not args.save_empty:

From b89caaee3b361e38d393ba9f8cd8f3d7d35938f1 Mon Sep 17 00:00:00 2001
From: gagnonanthony <79757265+gagnonanthony@users.noreply.github.com>
Date: Wed, 6 Dec 2023 02:35:59 +0000
Subject: [PATCH 14/97] add perp_diff to priors

---
 scripts/scil_compute_NODDI_priors.py | 53 ++++++++++++++++++++--------
 1 file changed, 38 insertions(+), 15 deletions(-)

diff --git a/scripts/scil_compute_NODDI_priors.py b/scripts/scil_compute_NODDI_priors.py
index 02f455376..1a119c175 100755
--- a/scripts/scil_compute_NODDI_priors.py
+++ b/scripts/scil_compute_NODDI_priors.py
@@ -2,7 +2,8 @@
 # -*- coding: utf-8 -*-
 
 """
-Compute the axial (para_diff) and mean (iso_diff) diffusivity priors for NODDI.
+Compute the axial (para_diff), radial (perp_diff), 
+and mean (iso_diff) diffusivity priors for NODDI.
 """
 
 import argparse
@@ -35,6 +36,8 @@ def _build_arg_parser():
                    help='Path to the FA volume.')
     p.add_argument('in_AD',
                    help='Path to the axial diffusivity (AD) volume.')
+    p.add_argument('in_RD',
+                   help='Path to the radial diffusivity (RD) volume.')
     p.add_argument('in_MD',
                    help='Path to the mean diffusivity (MD) volume.')
 
@@ -64,17 +67,21 @@ def _build_arg_parser():
              'priors. [center of the 3D volume]')
 
     g3 = p.add_argument_group('Outputs')
-    g3.add_argument('--out_txt_1fiber', metavar='FILE',
+    g3.add_argument('--out_txt_1fiber_para', metavar='FILE',
                     help='Output path for the text file containing the single '
-                         'fiber average value of AD.\nIf not set, the file will not '
-                         'be saved.')
+                         'fiber average value of AD.\nIf not set, the file '
+                         'will not be saved.')
+    g3.add_argument('--out_txt_1fiber_perp', metavar='FILE',
+                    help='Output path for the text file containing the single '
+                         'fiber average value of RD.\nIf not set, the file '
+                         'will not be saved.')
     g3.add_argument('--out_mask_1fiber', metavar='FILE',
                     help='Output path for single fiber mask. If not set, the '
                          'mask will not be saved.')
     g3.add_argument('--out_txt_ventricles', metavar='FILE',
                     help='Output path for the text file containing the '
-                         'ventricles average value of MD.\nIf not set, the file '
-                         'will not be saved.')
+                         'ventricles average value of MD.\nIf not set, the '
+                         'file will not be saved.')
     g3.add_argument('--out_mask_ventricles', metavar='FILE',
                     help='Output path for the ventricule mask.\nIf not set, '
                          'the mask will not be saved.')
@@ -89,14 +96,16 @@ def main():
     parser = _build_arg_parser()
     args = parser.parse_args()
 
-    assert_inputs_exist(parser, [args.in_AD, args.in_FA, args.in_MD])
+    assert_inputs_exist(parser, [args.in_AD, args.in_FA, args.in_MD,
+                                 args.in_RD])
     assert_outputs_exist(parser, args, [],
                          [args.out_mask_1fiber,
                           args.out_mask_ventricles,
                           args.out_txt_ventricles,
-                          args.out_txt_1fiber])
+                          args.out_txt_1fiber_para,
+                          args.out_txt_1fiber_perp])
 
-    assert_same_resolution([args.in_AD, args.in_FA, args.in_MD])
+    assert_same_resolution([args.in_AD, args.in_FA, args.in_MD, args.in_RD])
 
     log_level = logging.DEBUG if args.verbose else logging.INFO
     logging.getLogger().setLevel(log_level)
@@ -107,6 +116,7 @@ def main():
 
     md_data = nib.load(args.in_MD).get_fdata(dtype=np.float32)
     ad_data = nib.load(args.in_AD).get_fdata(dtype=np.float32)
+    rd_data = nib.load(args.in_RD).get_fdata(dtype=np.float32)
 
     mask_cc = np.zeros(fa_data.shape, dtype=np.uint8)
     mask_vent = np.zeros(fa_data.shape, dtype=np.uint8)
@@ -127,6 +137,9 @@ def main():
     roi_ad = ad_data[max(int(ci - w), 0): min(int(ci + w), fa_shape[0]),
                      max(int(cj - w), 0): min(int(cj + w), fa_shape[1]),
                      max(int(ck - w), 0): min(int(ck + w), fa_shape[2])]
+    roi_rd = rd_data[max(int(ci - w), 0): min(int(ci + w), fa_shape[0]),
+                     max(int(cj - w), 0): min(int(cj + w), fa_shape[1]),
+                     max(int(ck - w), 0): min(int(ck + w), fa_shape[2])]
     roi_md = md_data[max(int(ci - w), 0): min(int(ci + w), fa_shape[0]),
                      max(int(cj - w), 0): min(int(cj + w), fa_shape[1]),
                      max(int(ck - w), 0): min(int(ck + w), fa_shape[2])]
@@ -142,8 +155,11 @@ def main():
 
     logging.debug('Number of voxels found in single fiber area: {}'.format(N))
 
-    cc_avg = np.mean(roi_ad[indices])
-    cc_std = np.std(roi_ad[indices])
+    cc_avg_para = np.mean(roi_ad[indices])
+    cc_std_para = np.std(roi_ad[indices])
+    
+    cc_avg_perp = np.mean(roi_rd[indices])
+    cc_std_perp = np.std(roi_rd[indices])
 
     indices[0][:] += ci - w
     indices[1][:] += cj - w
@@ -169,14 +185,21 @@ def main():
     if args.out_mask_ventricles:
         nib.save(nib.Nifti1Image(mask_vent, affine), args.out_mask_ventricles)
 
-    if args.out_txt_1fiber:
-        np.savetxt(args.out_txt_1fiber, [cc_avg], fmt='%f')
+    if args.out_txt_1fiber_para:
+        np.savetxt(args.out_txt_1fiber_para, [cc_avg_para], fmt='%f')
+    
+    if args.out_txt_1fiber_perp:
+        np.savetxt(args.out_txt_1fiber_perp, [cc_avg_perp], fmt='%f')
 
     if args.out_txt_ventricles:
         np.savetxt(args.out_txt_ventricles, [vent_avg], fmt='%f')
 
-    logging.info("Average AD in single fiber areas: {} +- {}".format(cc_avg,
-                                                                     cc_std))
+    logging.info("Average AD in single fiber areas: {} +- {}".format(
+                                                                cc_avg_para,
+                                                                cc_std_para))
+    logging.info("Average RD in single fiber areas: {} +- {}".format(
+                                                                cc_avg_perp,
+                                                                cc_std_perp))
     logging.info("Average MD in ventricles: {} +- {}".format(vent_avg,
                                                              vent_std))
 

From 0e6fb5a5d406122f537a3fe6c1881a11c39e3e16 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <graham.little.phd@gmail.com>
Date: Thu, 14 Dec 2023 09:56:18 -0500
Subject: [PATCH 15/97] moved project_metrics func to module

---
 scilpy/tractograms/streamline_operations.py | 65 +++++++++++++++++++
 scripts/scil_project_map_to_streamlines.py  | 70 +--------------------
 2 files changed, 66 insertions(+), 69 deletions(-)

diff --git a/scilpy/tractograms/streamline_operations.py b/scilpy/tractograms/streamline_operations.py
index c97936f44..0fea389e3 100644
--- a/scilpy/tractograms/streamline_operations.py
+++ b/scilpy/tractograms/streamline_operations.py
@@ -50,6 +50,71 @@ def _get_point_on_line(first_point, second_point, vox_lower_corner):
     return first_point + ray * (t0 + t1) / 2.
 
 
+def project_metric_to_streamlines(sft, metric, endpoints_only=False):
+    """
+    Projects a metric onto the points of streamlines.
+
+    Parameters
+    ----------
+    sft: StatefulTractogram
+        Input tractogram.
+    metric: DataVolume
+        Input metric.
+
+    Optional:
+    ---------
+    endpoints_only: bool
+        If True, will only project the metric onto the endpoints of the
+        streamlines (all values along streamlines set to zero). If False,
+        will project the metric onto all points of the streamlines.
+
+    Returns
+    -------
+    streamline_data:
+        metric projected to each point of the streamlines.
+    """
+    if len(metric.data.shape) == 4:
+        dimension = metric.data.shape[3]
+    else:
+        dimension = 1
+
+    streamline_data = []
+    if endpoints_only:
+        for s in sft.streamlines:
+            p1_data = metric.get_value_at_coordinate(
+                s[0][0], s[0][1], s[0][2],
+                space=sft.space, origin=sft.origin)
+            p2_data = metric.get_value_at_coordinate(
+                s[-1][0], s[-1][1], s[-1][2],
+                space=sft.space, origin=sft.origin)
+            thisstreamline_data = []
+            for p in s:
+                if dimension == 1:
+                    thisstreamline_data.append(0)
+                else:
+                    thisstreamline_data.append(
+                       np.asarray(np.repeat(0, p1_data.shape[0])))
+
+            thisstreamline_data[0] = p1_data
+            thisstreamline_data[-1] = p2_data
+            thisstreamline_data = np.asarray(thisstreamline_data)
+
+            streamline_data.append(
+                np.reshape(thisstreamline_data,
+                        (len(thisstreamline_data), dimension)))
+    else:
+        for s in sft.streamlines:
+            thisstreamline_data = []
+            for p in s:
+                thisstreamline_data.append(metric.get_value_at_coordinate(
+                    p[0], p[1], p[2], space=sft.space, origin=sft.origin))
+
+            streamline_data.append(
+                np.reshape(thisstreamline_data,
+                        (len(thisstreamline_data), dimension)))
+
+    return streamline_data
+
 def filter_streamlines_by_length(sft, min_length=0., max_length=np.inf):
     """
     Filter streamlines using minimum and max length.
diff --git a/scripts/scil_project_map_to_streamlines.py b/scripts/scil_project_map_to_streamlines.py
index 818700f84..724ad5dd1 100755
--- a/scripts/scil_project_map_to_streamlines.py
+++ b/scripts/scil_project_map_to_streamlines.py
@@ -11,10 +11,9 @@
 import argparse
 import logging
 
-from numpy import asarray, reshape, repeat
-
 from scilpy.io.image import load_img
 from scilpy.io.streamlines import load_tractogram_with_reference
+from scilpy.tractograms.streamline_operations import project_metric_to_streamlines
 from scilpy.io.utils import (add_overwrite_arg,
                              assert_inputs_exist,
                              assert_outputs_exist,
@@ -25,73 +24,6 @@
 
 from dipy.io.streamline import save_tractogram, StatefulTractogram
 
-
-def project_metric_to_streamlines(sft, metric, endpoints_only=False):
-    """
-    Projects a metric onto the points of streamlines.
-
-    Parameters
-    ----------
-    sft: StatefulTractogram
-        Input tractogram.
-    metric: DataVolume
-        Input metric.
-
-    Optional:
-    ---------
-    endpoints_only: bool
-        If True, will only project the metric onto the endpoints of the
-        streamlines (all values along streamlines set to zero). If False,
-        will project the metric onto all points of the streamlines.
-
-    Returns
-    -------
-    streamline_data:
-        metric projected to each point of the streamlines.
-    """
-    if len(metric.data.shape) == 4:
-        dimension = metric.data.shape[3]
-    else:
-        dimension = 1
-
-    streamline_data = []
-    if endpoints_only:
-        for s in sft.streamlines:
-            p1_data = metric.get_value_at_coordinate(
-                s[0][0], s[0][1], s[0][2],
-                space=sft.space, origin=sft.origin)
-            p2_data = metric.get_value_at_coordinate(
-                s[-1][0], s[-1][1], s[-1][2],
-                space=sft.space, origin=sft.origin)
-            thisstreamline_data = []
-            for p in s:
-                if dimension == 1:
-                    thisstreamline_data.append(0)
-                else:
-                    thisstreamline_data.append(
-                        asarray(repeat(0, p1_data.shape[0])))
-
-            thisstreamline_data[0] = p1_data
-            thisstreamline_data[-1] = p2_data
-            thisstreamline_data = asarray(thisstreamline_data)
-
-            streamline_data.append(
-                reshape(thisstreamline_data,
-                        (len(thisstreamline_data), dimension)))
-    else:
-        for s in sft.streamlines:
-            thisstreamline_data = []
-            for p in s:
-                thisstreamline_data.append(metric.get_value_at_coordinate(
-                    p[0], p[1], p[2], space=sft.space, origin=sft.origin))
-
-            streamline_data.append(
-                reshape(thisstreamline_data,
-                        (len(thisstreamline_data), dimension)))
-
-    return streamline_data
-
-
 def _build_arg_parser():
     p = argparse.ArgumentParser(
         description=__doc__,

From 53ec9cc1ea79ff8bf21c9b1781e4421c1c168c98 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <graham.little.phd@gmail.com>
Date: Thu, 14 Dec 2023 10:17:12 -0500
Subject: [PATCH 16/97] moved streamline ops to module

---
 scilpy/tractograms/streamline_operations.py | 269 +++++++++++++++-----
 scripts/scil_streamlines_point_math.py      | 148 +----------
 2 files changed, 208 insertions(+), 209 deletions(-)

diff --git a/scilpy/tractograms/streamline_operations.py b/scilpy/tractograms/streamline_operations.py
index 0fea389e3..7b7dcab36 100644
--- a/scilpy/tractograms/streamline_operations.py
+++ b/scilpy/tractograms/streamline_operations.py
@@ -49,72 +49,6 @@ def _get_point_on_line(first_point, second_point, vox_lower_corner):
 
     return first_point + ray * (t0 + t1) / 2.
 
-
-def project_metric_to_streamlines(sft, metric, endpoints_only=False):
-    """
-    Projects a metric onto the points of streamlines.
-
-    Parameters
-    ----------
-    sft: StatefulTractogram
-        Input tractogram.
-    metric: DataVolume
-        Input metric.
-
-    Optional:
-    ---------
-    endpoints_only: bool
-        If True, will only project the metric onto the endpoints of the
-        streamlines (all values along streamlines set to zero). If False,
-        will project the metric onto all points of the streamlines.
-
-    Returns
-    -------
-    streamline_data:
-        metric projected to each point of the streamlines.
-    """
-    if len(metric.data.shape) == 4:
-        dimension = metric.data.shape[3]
-    else:
-        dimension = 1
-
-    streamline_data = []
-    if endpoints_only:
-        for s in sft.streamlines:
-            p1_data = metric.get_value_at_coordinate(
-                s[0][0], s[0][1], s[0][2],
-                space=sft.space, origin=sft.origin)
-            p2_data = metric.get_value_at_coordinate(
-                s[-1][0], s[-1][1], s[-1][2],
-                space=sft.space, origin=sft.origin)
-            thisstreamline_data = []
-            for p in s:
-                if dimension == 1:
-                    thisstreamline_data.append(0)
-                else:
-                    thisstreamline_data.append(
-                       np.asarray(np.repeat(0, p1_data.shape[0])))
-
-            thisstreamline_data[0] = p1_data
-            thisstreamline_data[-1] = p2_data
-            thisstreamline_data = np.asarray(thisstreamline_data)
-
-            streamline_data.append(
-                np.reshape(thisstreamline_data,
-                        (len(thisstreamline_data), dimension)))
-    else:
-        for s in sft.streamlines:
-            thisstreamline_data = []
-            for p in s:
-                thisstreamline_data.append(metric.get_value_at_coordinate(
-                    p[0], p[1], p[2], space=sft.space, origin=sft.origin))
-
-            streamline_data.append(
-                np.reshape(thisstreamline_data,
-                        (len(thisstreamline_data), dimension)))
-
-    return streamline_data
-
 def filter_streamlines_by_length(sft, min_length=0., max_length=np.inf):
     """
     Filter streamlines using minimum and max length.
@@ -445,3 +379,206 @@ def smooth_line_spline(streamline, sigma, nb_ctrl_points):
     smoothed_streamline[-1] = streamline[-1]
 
     return smoothed_streamline
+
+
+def perform_streamline_operation_per_point(op_name, sft, dpp_name='metric',
+                                                      endpoints_only=False):
+    """Peforms an operation per point for all streamlines.
+
+    Parameters
+    ----------
+    op_name: str
+        A callable that takes a list of streamline data per point (4D) and
+        returns a list of streamline data per point.
+    sft: StatefulTractogram
+        The streamlines used in the operation.
+    dpp_name: str
+        The name of the data per point to be used in the operation.
+    endpoints_only: bool
+        If True, will only perform operation on endpoints
+
+    Returns
+    -------
+    new_sft: StatefulTractogram
+        sft with data per streamline resulting from the operation.
+    """
+    # Performing operation
+    call_op = OPERATIONS[op_name]
+    if endpoints_only:
+        new_data_per_point = []
+        for s in sft.data_per_point[dpp_name]:
+            this_data_per_point = []
+            for p in s:
+                this_data_per_point.append(np.asarray(0.))
+            this_data_per_point[0] = call_op(s[0])
+            this_data_per_point[-1] = call_op(s[-1])
+            new_data_per_point.append(
+                np.reshape(this_data_per_point, (len(this_data_per_point), 1)))
+    else:
+        new_data_per_point = []
+        for s in sft.data_per_point[dpp_name]:
+            this_data_per_point = []
+            for p in s:
+                this_data_per_point.append(call_op(p))
+            new_data_per_point.append(
+                np.reshape(this_data_per_point, (len(this_data_per_point), 1)))
+
+    # Extracting streamlines
+    return new_data_per_point
+
+
+def perform_operation_per_streamline(op_name, sft, dpp_name='metric',
+                                                endpoints_only=False):
+    """Peforms an operation across points for each streamline.
+
+    Parameters
+    ----------
+    op_name: str
+        A callable that takes a list of streamline data per streamline and
+        returns a list of data per streamline.
+    sft: StatefulTractogram
+        The streamlines used in the operation.
+    dpp_name: str
+        The name of the data per point to be used in the operation.
+    endpoints_only: bool
+        If True, will only perform operation on endpoints
+
+    Returns
+    -------
+    new_sft: StatefulTractogram
+        sft with data per streamline resulting from the operation.
+    """
+    # Performing operation
+    call_op = OPERATIONS[op_name]
+    if endpoints_only:
+        new_data_per_streamline = []
+        for s in sft.data_per_point[dpp_name]:
+            new_data_per_streamline.append(call_op([s[0], s[-1]]))
+    else:
+        new_data_per_streamline = []
+        for s in sft.data_per_point[dpp_name]:
+            new_data_per_streamline.append(call_op(s))
+
+    return new_data_per_streamline
+
+
+def perform_streamline_operation_on_endpoints(op_name, sft, dpp_name='metric'):
+    """Peforms an operation across endpoints for each streamline.
+
+    Parameters
+    ----------
+    op_name: str
+        A callable that takes a list of streamline data per streamline and
+        returns a list of data per streamline.
+    sft: StatefulTractogram
+        The streamlines used in the operation.
+    dpp_name: str
+        The name of the data per point to be used in the operation.
+
+    Returns
+    -------
+    new_sft: StatefulTractogram
+        sft with data per streamline resulting from the operation.
+    """
+    # Performing operation
+    call_op = OPERATIONS[op_name]
+    new_data_per_streamline = []
+    for s in sft.data_per_point[dpp_name]:
+        new_data_per_streamline.append(call_op(s[0], s[-1])[0, 1])
+
+    return new_data_per_streamline
+
+
+def mean(array):
+    return np.mean(array)
+
+
+def sum(array):
+    return np.sum(array)
+
+
+def min(array):
+    return np.min(array)
+
+
+def max(array):
+    return np.max(array)
+
+
+def correlation(array1, array2):
+    return np.corrcoef(array1, array2)
+
+
+OPERATIONS = {
+    'mean': mean,
+    'sum': sum,
+    'min': min,
+    'max': max,
+    'correlation': correlation,
+}
+
+
+def project_metric_to_streamlines(sft, metric, endpoints_only=False):
+    """
+    Projects a metric onto the points of streamlines.
+
+    Parameters
+    ----------
+    sft: StatefulTractogram
+        Input tractogram.
+    metric: DataVolume
+        Input metric.
+
+    Optional:
+    ---------
+    endpoints_only: bool
+        If True, will only project the metric onto the endpoints of the
+        streamlines (all values along streamlines set to zero). If False,
+        will project the metric onto all points of the streamlines.
+
+    Returns
+    -------
+    streamline_data:
+        metric projected to each point of the streamlines.
+    """
+    if len(metric.data.shape) == 4:
+        dimension = metric.data.shape[3]
+    else:
+        dimension = 1
+
+    streamline_data = []
+    if endpoints_only:
+        for s in sft.streamlines:
+            p1_data = metric.get_value_at_coordinate(
+                s[0][0], s[0][1], s[0][2],
+                space=sft.space, origin=sft.origin)
+            p2_data = metric.get_value_at_coordinate(
+                s[-1][0], s[-1][1], s[-1][2],
+                space=sft.space, origin=sft.origin)
+            thisstreamline_data = []
+            for p in s:
+                if dimension == 1:
+                    thisstreamline_data.append(0)
+                else:
+                    thisstreamline_data.append(
+                        np.asarray(np.repeat(0, p1_data.shape[0])))
+
+            thisstreamline_data[0] = p1_data
+            thisstreamline_data[-1] = p2_data
+            thisstreamline_data = np.asarray(thisstreamline_data)
+
+            streamline_data.append(
+                np.reshape(thisstreamline_data,
+                           (len(thisstreamline_data), dimension)))
+    else:
+        for s in sft.streamlines:
+            thisstreamline_data = []
+            for p in s:
+                thisstreamline_data.append(metric.get_value_at_coordinate(
+                    p[0], p[1], p[2], space=sft.space, origin=sft.origin))
+
+            streamline_data.append(
+                np.reshape(thisstreamline_data,
+                           (len(thisstreamline_data), dimension)))
+
+    return streamline_data
diff --git a/scripts/scil_streamlines_point_math.py b/scripts/scil_streamlines_point_math.py
index 5bbad7deb..463de8504 100755
--- a/scripts/scil_streamlines_point_math.py
+++ b/scripts/scil_streamlines_point_math.py
@@ -32,11 +32,7 @@
 import argparse
 import logging
 
-from copy import deepcopy
-
 from dipy.io.streamline import save_tractogram, StatefulTractogram
-import numpy as np
-from numpy import asarray, reshape
 
 from scilpy.io.streamlines import load_tractogram_with_reference
 from scilpy.io.utils import (add_bbox_arg,
@@ -46,143 +42,9 @@
                              assert_inputs_exist,
                              assert_outputs_exist)
 
-
-def perform_operation_per_point(op_name, sft, dpp_name='metric',
-                                endpoints_only=False):
-    """Peforms an operation per point for all streamlines.
-
-    Parameters
-    ----------
-    op_name: str
-        A callable that takes a list of streamline data per point (4D) and
-        returns a list of streamline data per point.
-    sft: StatefulTractogram
-        The streamlines used in the operation.
-    dpp_name: str
-        The name of the data per point to be used in the operation.
-    endpoints_only: bool
-        If True, will only perform operation on endpoints
-
-    Returns
-    -------
-    new_sft: StatefulTractogram
-        sft with data per streamline resulting from the operation.
-    """
-    # Performing operation
-    call_op = OPERATIONS[op_name]
-    if endpoints_only:
-        new_data_per_point = []
-        for s in sft.data_per_point[dpp_name]:
-            this_data_per_point = []
-            for p in s:
-                this_data_per_point.append(asarray(0.))
-            this_data_per_point[0] = call_op(s[0])
-            this_data_per_point[-1] = call_op(s[-1])
-            new_data_per_point.append(
-                reshape(this_data_per_point, (len(this_data_per_point), 1)))
-    else:
-        new_data_per_point = []
-        for s in sft.data_per_point[dpp_name]:
-            this_data_per_point = []
-            for p in s:
-                this_data_per_point.append(call_op(p))
-            new_data_per_point.append(
-                reshape(this_data_per_point, (len(this_data_per_point), 1)))
-
-    # Extracting streamlines
-    return new_data_per_point
-
-
-def perform_operation_per_streamline(op_name, sft, dpp_name='metric',
-                                     endpoints_only=False):
-    """Peforms an operation across points for each streamline.
-
-    Parameters
-    ----------
-    op_name: str
-        A callable that takes a list of streamline data per streamline and
-        returns a list of data per streamline.
-    sft: StatefulTractogram
-        The streamlines used in the operation.
-    dpp_name: str
-        The name of the data per point to be used in the operation.
-    endpoints_only: bool
-        If True, will only perform operation on endpoints
-
-    Returns
-    -------
-    new_sft: StatefulTractogram
-        sft with data per streamline resulting from the operation.
-    """
-    # Performing operation
-    call_op = OPERATIONS[op_name]
-    if endpoints_only:
-        new_data_per_streamline = []
-        for s in sft.data_per_point[dpp_name]:
-            new_data_per_streamline.append(call_op([s[0], s[-1]]))
-    else:
-        new_data_per_streamline = []
-        for s in sft.data_per_point[dpp_name]:
-            new_data_per_streamline.append(call_op(s))
-
-    return new_data_per_streamline
-
-
-def perform_operation_across_endpoints(op_name, sft, dpp_name='metric'):
-    """Peforms an operation across endpoints for each streamline.
-
-    Parameters
-    ----------
-    op_name: str
-        A callable that takes a list of streamline data per streamline and
-        returns a list of data per streamline.
-    sft: StatefulTractogram
-        The streamlines used in the operation.
-    dpp_name: str
-        The name of the data per point to be used in the operation.
-
-    Returns
-    -------
-    new_sft: StatefulTractogram
-        sft with data per streamline resulting from the operation.
-    """
-    # Performing operation
-    call_op = OPERATIONS[op_name]
-    new_data_per_streamline = []
-    for s in sft.data_per_point[dpp_name]:
-        new_data_per_streamline.append(call_op(s[0], s[-1])[0, 1])
-
-    return new_data_per_streamline
-
-
-def mean(array):
-    return np.mean(array)
-
-
-def sum(array):
-    return np.sum(array)
-
-
-def min(array):
-    return np.min(array)
-
-
-def max(array):
-    return np.max(array)
-
-
-def correlation(array1, array2):
-    return np.corrcoef(array1, array2)
-
-
-OPERATIONS = {
-    'mean': mean,
-    'sum': sum,
-    'min': min,
-    'max': max,
-    'correlation': correlation,
-}
-
+from scilpy.tractograms.streamline_operations import (perform_streamline_operation_on_endpoints,
+     perform_streamline_operation_per_point,
+     perform_operation_per_streamline)
 
 def _build_arg_parser():
     p = argparse.ArgumentParser(
@@ -262,7 +124,7 @@ def main():
         if args.operation == 'correlation':
             logging.info('Performing {} across endpoint data.'.format(
                 args.operation))
-            new_data_per_streamline = perform_operation_across_endpoints(
+            new_data_per_streamline = perform_streamline_operation_on_endpoints(
                 args.operation, sft, args.dpp_name)
 
             # Adding data per streamline to new_sft
@@ -277,7 +139,7 @@ def main():
             logging.info(
                 'Performing {} on data from each streamine point.'.format(
                     args.operation))
-            new_data_per_point = perform_operation_per_point(
+            new_data_per_point = perform_streamline_operation_per_point(
                 args.operation, sft, args.dpp_name, args.endpoints_only)
 
             # Adding data per point to new_sft

From 061f3998123fa16ea34e48c1fd953989aa3426ea Mon Sep 17 00:00:00 2001
From: grahamlittlephd <graham.little.phd@gmail.com>
Date: Thu, 14 Dec 2023 10:28:17 -0500
Subject: [PATCH 17/97] added blank unit tests

---
 scilpy/tractograms/streamline_operations.py   |  1 +
 .../tests/tests_streamline_operations.py      | 21 +++++++++++++++++++
 2 files changed, 22 insertions(+)

diff --git a/scilpy/tractograms/streamline_operations.py b/scilpy/tractograms/streamline_operations.py
index 7b7dcab36..552609d49 100644
--- a/scilpy/tractograms/streamline_operations.py
+++ b/scilpy/tractograms/streamline_operations.py
@@ -402,6 +402,7 @@ def perform_streamline_operation_per_point(op_name, sft, dpp_name='metric',
     new_sft: StatefulTractogram
         sft with data per streamline resulting from the operation.
     """
+    
     # Performing operation
     call_op = OPERATIONS[op_name]
     if endpoints_only:
diff --git a/scilpy/tractograms/tests/tests_streamline_operations.py b/scilpy/tractograms/tests/tests_streamline_operations.py
index e0714f420..4029cd4bf 100644
--- a/scilpy/tractograms/tests/tests_streamline_operations.py
+++ b/scilpy/tractograms/tests/tests_streamline_operations.py
@@ -58,3 +58,24 @@ def test_resample_streamlines_step_size():
 def compute_streamline_segment():
     # toDo
     pass
+
+
+def test_project_metric_to_streamlines():
+    # toDo
+    pass
+
+
+def test_perform_streamline_operation_per_point():
+    # toDo
+    pass
+
+
+def test_perform_operation_per_streamline():
+    # toDo
+    pass
+
+
+def test_perform_streamline_operation_on_endpoints():
+    # toDo
+    pass
+

From c8b38895a1d076f16e041f8139203ee836a354c4 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <graham.little.phd@gmail.com>
Date: Thu, 14 Dec 2023 11:24:05 -0500
Subject: [PATCH 18/97] added script test

---
 .../tests/test_project_map_to_streamlines.py  | 84 +++++++++++++++++++
 1 file changed, 84 insertions(+)
 create mode 100644 scripts/tests/test_project_map_to_streamlines.py

diff --git a/scripts/tests/test_project_map_to_streamlines.py b/scripts/tests/test_project_map_to_streamlines.py
new file mode 100644
index 000000000..9f2f417f3
--- /dev/null
+++ b/scripts/tests/test_project_map_to_streamlines.py
@@ -0,0 +1,84 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import os
+import tempfile
+
+from scilpy.io.fetcher import fetch_data, get_home, get_testing_files_dict
+
+# If they already exist, this only takes 5 seconds (check md5sum)
+fetch_data(get_testing_files_dict(), keys=['others.zip'])
+tmp_dir = tempfile.TemporaryDirectory()
+
+
+##### Deprecated file but it should still be running.
+##### For more exhaustive tests, see test_tractogram_math.py
+
+def test_help_option(script_runner):
+    ret = script_runner.run('scil_project_map_to_streamlines.py', '--help')
+    assert ret.success
+
+
+def test_execution_3D_map(script_runner):
+    os.chdir(os.path.expanduser(tmp_dir.name))
+    in_fa = os.path.join(get_home(), 'others', 'fa.nii.gz')
+    in_tracto_1 = os.path.join(get_home(), 'others',
+                               'IFGWM_sub.trk')
+
+    ret = script_runner.run('scil_project_map_to_streamlines.py',
+                            in_tracto_1, in_fa, 'fa_on_streamlines.trk')
+    assert ret.success
+
+def test_execution_4D_map(script_runner):
+    os.chdir(os.path.expanduser(tmp_dir.name))
+    in_rgb = os.path.join(get_home(), 'others', 'rgb.nii.gz')
+    in_tracto_1 = os.path.join(get_home(), 'others',
+                               'IFGWM_sub.trk')
+
+    ret = script_runner.run('scil_project_map_to_streamlines.py',
+                            in_tracto_1, in_rgb, 'rgb_on_streamlines.trk')
+    assert ret.success
+
+def test_execution_3D_map_endpoints_only(script_runner):
+    os.chdir(os.path.expanduser(tmp_dir.name))
+    in_fa = os.path.join(get_home(), 'others', 'fa.nii.gz')
+    in_tracto_1 = os.path.join(get_home(), 'others',
+                               'IFGWM_sub.trk')
+
+    ret = script_runner.run('scil_project_map_to_streamlines.py',
+                            in_tracto_1, in_fa, 'fa_on_streamlines.trk',
+                            '--endpoints_only')
+    assert ret.success
+
+def test_execution_4D_map_endpoints_only(script_runner):
+    os.chdir(os.path.expanduser(tmp_dir.name))
+    in_rgb = os.path.join(get_home(), 'others', 'rgb.nii.gz')
+    in_tracto_1 = os.path.join(get_home(), 'others',
+                               'IFGWM_sub.trk')
+
+    ret = script_runner.run('scil_project_map_to_streamlines.py',
+                            in_tracto_1, in_rgb, 'rgb_on_streamlines.trk',
+                            '--endpoints_only')
+    assert ret.success
+
+def test_execution_3D_map_dpp_name(script_runner):
+    os.chdir(os.path.expanduser(tmp_dir.name))
+    in_fa = os.path.join(get_home(), 'others', 'fa.nii.gz')
+    in_tracto_1 = os.path.join(get_home(), 'others',
+                               'IFGWM_sub.trk')
+
+    ret = script_runner.run('scil_project_map_to_streamlines.py',
+                            in_tracto_1, in_fa, 'fa_on_streamlines.trk',
+                            '--dpp_name', 'fa')
+    assert ret.success
+
+def test_execution_3D_map_trilinear(script_runner):
+    os.chdir(os.path.expanduser(tmp_dir.name))
+    in_fa = os.path.join(get_home(), 'others', 'fa.nii.gz')
+    in_tracto_1 = os.path.join(get_home(), 'others',
+                               'IFGWM_sub.trk')
+
+    ret = script_runner.run('scil_project_map_to_streamlines.py',
+                            in_tracto_1, in_fa, 'fa_on_streamlines.trk',
+                            '--trilinear')
+    assert ret.success
\ No newline at end of file

From 1f0ac45cab3b56fdcf162d497f35f235cd8e10a2 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <graham.little.phd@gmail.com>
Date: Thu, 14 Dec 2023 11:56:09 -0500
Subject: [PATCH 19/97] renamed scripts

---
 ...il_streamlines_point_math.py => scil_tractogram_point_math.py} | 0
 ...reamlines.py => scil_tractogram_project_map_to_streamlines.py} | 0
 ...reamlines.py => test_tractogram_project_map_to_streamlines.py} | 0
 3 files changed, 0 insertions(+), 0 deletions(-)
 rename scripts/{scil_streamlines_point_math.py => scil_tractogram_point_math.py} (100%)
 rename scripts/{scil_project_map_to_streamlines.py => scil_tractogram_project_map_to_streamlines.py} (100%)
 rename scripts/tests/{test_project_map_to_streamlines.py => test_tractogram_project_map_to_streamlines.py} (100%)

diff --git a/scripts/scil_streamlines_point_math.py b/scripts/scil_tractogram_point_math.py
similarity index 100%
rename from scripts/scil_streamlines_point_math.py
rename to scripts/scil_tractogram_point_math.py
diff --git a/scripts/scil_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
similarity index 100%
rename from scripts/scil_project_map_to_streamlines.py
rename to scripts/scil_tractogram_project_map_to_streamlines.py
diff --git a/scripts/tests/test_project_map_to_streamlines.py b/scripts/tests/test_tractogram_project_map_to_streamlines.py
similarity index 100%
rename from scripts/tests/test_project_map_to_streamlines.py
rename to scripts/tests/test_tractogram_project_map_to_streamlines.py

From 44fe6976bcdddbaffa03728272ed2f7865d02da9 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <graham.little.phd@gmail.com>
Date: Thu, 14 Dec 2023 11:58:33 -0500
Subject: [PATCH 20/97] update naming in tests

---
 .../test_tractogram_project_map_to_streamlines.py  | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/scripts/tests/test_tractogram_project_map_to_streamlines.py b/scripts/tests/test_tractogram_project_map_to_streamlines.py
index 9f2f417f3..d6c744191 100644
--- a/scripts/tests/test_tractogram_project_map_to_streamlines.py
+++ b/scripts/tests/test_tractogram_project_map_to_streamlines.py
@@ -15,7 +15,7 @@
 ##### For more exhaustive tests, see test_tractogram_math.py
 
 def test_help_option(script_runner):
-    ret = script_runner.run('scil_project_map_to_streamlines.py', '--help')
+    ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py', '--help')
     assert ret.success
 
 
@@ -25,7 +25,7 @@ def test_execution_3D_map(script_runner):
     in_tracto_1 = os.path.join(get_home(), 'others',
                                'IFGWM_sub.trk')
 
-    ret = script_runner.run('scil_project_map_to_streamlines.py',
+    ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
                             in_tracto_1, in_fa, 'fa_on_streamlines.trk')
     assert ret.success
 
@@ -35,7 +35,7 @@ def test_execution_4D_map(script_runner):
     in_tracto_1 = os.path.join(get_home(), 'others',
                                'IFGWM_sub.trk')
 
-    ret = script_runner.run('scil_project_map_to_streamlines.py',
+    ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
                             in_tracto_1, in_rgb, 'rgb_on_streamlines.trk')
     assert ret.success
 
@@ -45,7 +45,7 @@ def test_execution_3D_map_endpoints_only(script_runner):
     in_tracto_1 = os.path.join(get_home(), 'others',
                                'IFGWM_sub.trk')
 
-    ret = script_runner.run('scil_project_map_to_streamlines.py',
+    ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
                             in_tracto_1, in_fa, 'fa_on_streamlines.trk',
                             '--endpoints_only')
     assert ret.success
@@ -56,7 +56,7 @@ def test_execution_4D_map_endpoints_only(script_runner):
     in_tracto_1 = os.path.join(get_home(), 'others',
                                'IFGWM_sub.trk')
 
-    ret = script_runner.run('scil_project_map_to_streamlines.py',
+    ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
                             in_tracto_1, in_rgb, 'rgb_on_streamlines.trk',
                             '--endpoints_only')
     assert ret.success
@@ -67,7 +67,7 @@ def test_execution_3D_map_dpp_name(script_runner):
     in_tracto_1 = os.path.join(get_home(), 'others',
                                'IFGWM_sub.trk')
 
-    ret = script_runner.run('scil_project_map_to_streamlines.py',
+    ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
                             in_tracto_1, in_fa, 'fa_on_streamlines.trk',
                             '--dpp_name', 'fa')
     assert ret.success
@@ -78,7 +78,7 @@ def test_execution_3D_map_trilinear(script_runner):
     in_tracto_1 = os.path.join(get_home(), 'others',
                                'IFGWM_sub.trk')
 
-    ret = script_runner.run('scil_project_map_to_streamlines.py',
+    ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
                             in_tracto_1, in_fa, 'fa_on_streamlines.trk',
                             '--trilinear')
     assert ret.success
\ No newline at end of file

From a5f67a7e7837554ea4216857039c6f1e6ca84020 Mon Sep 17 00:00:00 2001
From: gagnonanthony <79757265+gagnonanthony@users.noreply.github.com>
Date: Tue, 19 Dec 2023 15:42:06 -0500
Subject: [PATCH 21/97] update test + pep8

---
 scripts/scil_NODDI_priors.py       |  6 +++---
 scripts/tests/test_NODDI_priors.py | 15 +++++++++------
 2 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/scripts/scil_NODDI_priors.py b/scripts/scil_NODDI_priors.py
index d21f28b34..297c730bb 100755
--- a/scripts/scil_NODDI_priors.py
+++ b/scripts/scil_NODDI_priors.py
@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 
 """
-Compute the axial (para_diff), radial (perp_diff), 
+Compute the axial (para_diff), radial (perp_diff),
 and mean (iso_diff) diffusivity priors for NODDI.
 """
 
@@ -157,7 +157,7 @@ def main():
 
     cc_avg_para = np.mean(roi_ad[indices])
     cc_std_para = np.std(roi_ad[indices])
-    
+
     cc_avg_perp = np.mean(roi_rd[indices])
     cc_std_perp = np.std(roi_rd[indices])
 
@@ -187,7 +187,7 @@ def main():
 
     if args.out_txt_1fiber_para:
         np.savetxt(args.out_txt_1fiber_para, [cc_avg_para], fmt='%f')
-    
+
     if args.out_txt_1fiber_perp:
         np.savetxt(args.out_txt_1fiber_perp, [cc_avg_perp], fmt='%f')
 
diff --git a/scripts/tests/test_NODDI_priors.py b/scripts/tests/test_NODDI_priors.py
index 7ce35481f..577ee2f9e 100644
--- a/scripts/tests/test_NODDI_priors.py
+++ b/scripts/tests/test_NODDI_priors.py
@@ -7,7 +7,7 @@
 from scilpy.io.fetcher import fetch_data, get_home, get_testing_files_dict
 
 # If they already exist, this only takes 5 seconds (check md5sum)
-fetch_data(get_testing_files_dict(), keys=['commit_amico.zip'])
+fetch_data(get_testing_files_dict(), keys=['processing.zip'])
 tmp_dir = tempfile.TemporaryDirectory()
 
 
@@ -18,14 +18,17 @@ def test_help_option(script_runner):
 
 def test_execution_commit_amico(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
-    in_fa = os.path.join(get_home(), 'commit_amico',
+    in_fa = os.path.join(get_home(), 'processing',
                          'fa.nii.gz')
-    in_ad = os.path.join(get_home(), 'commit_amico',
+    in_ad = os.path.join(get_home(), 'processing',
                          'ad.nii.gz')
-    in_md = os.path.join(get_home(), 'commit_amico',
+    in_md = os.path.join(get_home(), 'processing',
                          'md.nii.gz')
-    ret = script_runner.run('scil_NODDI_priors.py', in_fa, in_ad, in_md,
-                            '--out_txt_1fiber', '1fiber.txt',
+    in_rd = os.path.join(get_home(), 'processing',
+                         'rd.nii.gz')
+    ret = script_runner.run('scil_NODDI_priors.py', in_fa, in_ad, in_rd, in_md,
+                            '--out_txt_1fiber_para', '1fiber_para.txt',
+                            '--out_txt_1fiber_perp', '1fiber_perp.txt',
                             '--out_mask_1fiber', '1fiber.nii.gz',
                             '--out_txt_ventricles', 'ventricules.txt',
                             '--out_mask_ventricles', 'ventricules.nii.gz')

From 16e308464e85d178c45d5e6dccf12a1aa5bb9ee9 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Wed, 10 Jan 2024 13:20:38 -0500
Subject: [PATCH 22/97] add blank unit tests to streamline operations

---
 .../tests/test_streamline_operations.py       | 20 +++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/scilpy/tractograms/tests/test_streamline_operations.py b/scilpy/tractograms/tests/test_streamline_operations.py
index faeb4e57c..b37c4aec7 100644
--- a/scilpy/tractograms/tests/test_streamline_operations.py
+++ b/scilpy/tractograms/tests/test_streamline_operations.py
@@ -367,3 +367,23 @@ def test_smooth_line_spline():
     dist_2 = np.linalg.norm(noisy_streamline - smoothed_streamline)
 
     assert dist_1 < dist_2
+
+
+def test_project_metric_to_streamlines():
+    # toDo
+    pass
+
+
+def test_perform_streamline_operation_per_point():
+    # toDo
+    pass
+
+
+def test_perform_operation_per_streamline():
+    # toDo
+    pass
+
+
+def test_perform_streamline_operation_on_endpoints():
+    # toDo
+    pass

From b5660fde0aea3a94438ddabf7777f7c7598d7df9 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <graham.little.phd@gmail.com>
Date: Thu, 11 Jan 2024 13:27:59 -0500
Subject: [PATCH 23/97] pep errors

---
 scilpy/tractograms/streamline_operations.py      |  6 +++---
 scripts/scil_tractogram_point_math.py            | 16 +++++++++-------
 ...scil_tractogram_project_map_to_streamlines.py |  3 ++-
 ...test_tractogram_project_map_to_streamlines.py | 14 ++++++++------
 4 files changed, 22 insertions(+), 17 deletions(-)

diff --git a/scilpy/tractograms/streamline_operations.py b/scilpy/tractograms/streamline_operations.py
index 6fb3197a4..212ff0ef4 100644
--- a/scilpy/tractograms/streamline_operations.py
+++ b/scilpy/tractograms/streamline_operations.py
@@ -391,7 +391,7 @@ def smooth_line_spline(streamline, smoothing_parameter, nb_ctrl_points):
 
 
 def perform_streamline_operation_per_point(op_name, sft, dpp_name='metric',
-                                                      endpoints_only=False):
+                                            endpoints_only=False):
     """Peforms an operation per point for all streamlines.
 
     Parameters
@@ -411,7 +411,7 @@ def perform_streamline_operation_per_point(op_name, sft, dpp_name='metric',
     new_sft: StatefulTractogram
         sft with data per streamline resulting from the operation.
     """
-    
+
     # Performing operation
     call_op = OPERATIONS[op_name]
     if endpoints_only:
@@ -438,7 +438,7 @@ def perform_streamline_operation_per_point(op_name, sft, dpp_name='metric',
 
 
 def perform_operation_per_streamline(op_name, sft, dpp_name='metric',
-                                                endpoints_only=False):
+                                    endpoints_only=False):
     """Peforms an operation across points for each streamline.
 
     Parameters
diff --git a/scripts/scil_tractogram_point_math.py b/scripts/scil_tractogram_point_math.py
index 463de8504..c9594d97c 100755
--- a/scripts/scil_tractogram_point_math.py
+++ b/scripts/scil_tractogram_point_math.py
@@ -42,9 +42,11 @@
                              assert_inputs_exist,
                              assert_outputs_exist)
 
-from scilpy.tractograms.streamline_operations import (perform_streamline_operation_on_endpoints,
-     perform_streamline_operation_per_point,
-     perform_operation_per_streamline)
+from scilpy.tractograms.streamline_operations import (
+        perform_streamline_operation_on_endpoints,
+        perform_streamline_operation_per_point,
+        perform_operation_per_streamline)
+
 
 def _build_arg_parser():
     p = argparse.ArgumentParser(
@@ -124,7 +126,7 @@ def main():
         if args.operation == 'correlation':
             logging.info('Performing {} across endpoint data.'.format(
                 args.operation))
-            new_data_per_streamline = perform_streamline_operation_on_endpoints(
+            new_dps= perform_streamline_operation_on_endpoints(
                 args.operation, sft, args.dpp_name)
 
             # Adding data per streamline to new_sft
@@ -133,13 +135,13 @@ def main():
                                          sft.space, sft.origin,
                                          data_per_streamline={
                                              args.output_dpp_name:
-                                             new_data_per_streamline})
+                                             new_dps})
         else:
             # Results in new data per point
             logging.info(
                 'Performing {} on data from each streamine point.'.format(
                     args.operation))
-            new_data_per_point = perform_streamline_operation_per_point(
+            new_dpp = perform_streamline_operation_per_point(
                 args.operation, sft, args.dpp_name, args.endpoints_only)
 
             # Adding data per point to new_sft
@@ -148,7 +150,7 @@ def main():
                                          sft.space, sft.origin,
                                          data_per_point={
                                              args.output_dpp_name:
-                                             new_data_per_point})
+                                             new_dpp})
     else:
         # Results in new data per streamline
         logging.info(
diff --git a/scripts/scil_tractogram_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
index 724ad5dd1..78f11dc3d 100755
--- a/scripts/scil_tractogram_project_map_to_streamlines.py
+++ b/scripts/scil_tractogram_project_map_to_streamlines.py
@@ -13,7 +13,8 @@
 
 from scilpy.io.image import load_img
 from scilpy.io.streamlines import load_tractogram_with_reference
-from scilpy.tractograms.streamline_operations import project_metric_to_streamlines
+from scilpy.tractograms.streamline_operations import (
+    project_metric_to_streamlines)
 from scilpy.io.utils import (add_overwrite_arg,
                              assert_inputs_exist,
                              assert_outputs_exist,
diff --git a/scripts/tests/test_tractogram_project_map_to_streamlines.py b/scripts/tests/test_tractogram_project_map_to_streamlines.py
index d6c744191..95d99000c 100644
--- a/scripts/tests/test_tractogram_project_map_to_streamlines.py
+++ b/scripts/tests/test_tractogram_project_map_to_streamlines.py
@@ -10,12 +10,9 @@
 fetch_data(get_testing_files_dict(), keys=['others.zip'])
 tmp_dir = tempfile.TemporaryDirectory()
 
-
-##### Deprecated file but it should still be running.
-##### For more exhaustive tests, see test_tractogram_math.py
-
 def test_help_option(script_runner):
-    ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py', '--help')
+    ret = script_runner.run(
+            'scil_tractogram_project_map_to_streamlines.py', '--help')
     assert ret.success
 
 
@@ -29,6 +26,7 @@ def test_execution_3D_map(script_runner):
                             in_tracto_1, in_fa, 'fa_on_streamlines.trk')
     assert ret.success
 
+
 def test_execution_4D_map(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_rgb = os.path.join(get_home(), 'others', 'rgb.nii.gz')
@@ -39,6 +37,7 @@ def test_execution_4D_map(script_runner):
                             in_tracto_1, in_rgb, 'rgb_on_streamlines.trk')
     assert ret.success
 
+
 def test_execution_3D_map_endpoints_only(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_fa = os.path.join(get_home(), 'others', 'fa.nii.gz')
@@ -50,6 +49,7 @@ def test_execution_3D_map_endpoints_only(script_runner):
                             '--endpoints_only')
     assert ret.success
 
+
 def test_execution_4D_map_endpoints_only(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_rgb = os.path.join(get_home(), 'others', 'rgb.nii.gz')
@@ -61,6 +61,7 @@ def test_execution_4D_map_endpoints_only(script_runner):
                             '--endpoints_only')
     assert ret.success
 
+
 def test_execution_3D_map_dpp_name(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_fa = os.path.join(get_home(), 'others', 'fa.nii.gz')
@@ -72,6 +73,7 @@ def test_execution_3D_map_dpp_name(script_runner):
                             '--dpp_name', 'fa')
     assert ret.success
 
+
 def test_execution_3D_map_trilinear(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_fa = os.path.join(get_home(), 'others', 'fa.nii.gz')
@@ -81,4 +83,4 @@ def test_execution_3D_map_trilinear(script_runner):
     ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
                             in_tracto_1, in_fa, 'fa_on_streamlines.trk',
                             '--trilinear')
-    assert ret.success
\ No newline at end of file
+    assert ret.success

From a0fc9929e8ac21215e1f52a916d9eea08e46615a Mon Sep 17 00:00:00 2001
From: grahamlittlephd <graham.little.phd@gmail.com>
Date: Thu, 11 Jan 2024 13:38:45 -0500
Subject: [PATCH 24/97] pep errors 2

---
 scilpy/tractograms/streamline_operations.py                 | 4 ++--
 scripts/scil_tractogram_point_math.py                       | 2 +-
 scripts/scil_tractogram_project_map_to_streamlines.py       | 1 +
 scripts/tests/test_tractogram_project_map_to_streamlines.py | 1 +
 4 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/scilpy/tractograms/streamline_operations.py b/scilpy/tractograms/streamline_operations.py
index 212ff0ef4..20d8be343 100644
--- a/scilpy/tractograms/streamline_operations.py
+++ b/scilpy/tractograms/streamline_operations.py
@@ -391,7 +391,7 @@ def smooth_line_spline(streamline, smoothing_parameter, nb_ctrl_points):
 
 
 def perform_streamline_operation_per_point(op_name, sft, dpp_name='metric',
-                                            endpoints_only=False):
+                                           endpoints_only=False):
     """Peforms an operation per point for all streamlines.
 
     Parameters
@@ -438,7 +438,7 @@ def perform_streamline_operation_per_point(op_name, sft, dpp_name='metric',
 
 
 def perform_operation_per_streamline(op_name, sft, dpp_name='metric',
-                                    endpoints_only=False):
+                                     endpoints_only=False):
     """Peforms an operation across points for each streamline.
 
     Parameters
diff --git a/scripts/scil_tractogram_point_math.py b/scripts/scil_tractogram_point_math.py
index c9594d97c..7adf7d61a 100755
--- a/scripts/scil_tractogram_point_math.py
+++ b/scripts/scil_tractogram_point_math.py
@@ -126,7 +126,7 @@ def main():
         if args.operation == 'correlation':
             logging.info('Performing {} across endpoint data.'.format(
                 args.operation))
-            new_dps= perform_streamline_operation_on_endpoints(
+            new_dps = perform_streamline_operation_on_endpoints(
                 args.operation, sft, args.dpp_name)
 
             # Adding data per streamline to new_sft
diff --git a/scripts/scil_tractogram_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
index 78f11dc3d..34ef2152c 100755
--- a/scripts/scil_tractogram_project_map_to_streamlines.py
+++ b/scripts/scil_tractogram_project_map_to_streamlines.py
@@ -25,6 +25,7 @@
 
 from dipy.io.streamline import save_tractogram, StatefulTractogram
 
+
 def _build_arg_parser():
     p = argparse.ArgumentParser(
         description=__doc__,
diff --git a/scripts/tests/test_tractogram_project_map_to_streamlines.py b/scripts/tests/test_tractogram_project_map_to_streamlines.py
index 95d99000c..c87c31b93 100644
--- a/scripts/tests/test_tractogram_project_map_to_streamlines.py
+++ b/scripts/tests/test_tractogram_project_map_to_streamlines.py
@@ -10,6 +10,7 @@
 fetch_data(get_testing_files_dict(), keys=['others.zip'])
 tmp_dir = tempfile.TemporaryDirectory()
 
+
 def test_help_option(script_runner):
     ret = script_runner.run(
             'scil_tractogram_project_map_to_streamlines.py', '--help')

From e1795fb3c2782501a1c05d3b6ec0a56e8030ab5f Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 15 Jan 2024 11:53:23 -0500
Subject: [PATCH 25/97] tests passed

---
 ...t_tractogram_project_map_to_streamlines.py | 20 +++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/scripts/tests/test_tractogram_project_map_to_streamlines.py b/scripts/tests/test_tractogram_project_map_to_streamlines.py
index c87c31b93..13dcf4fcb 100644
--- a/scripts/tests/test_tractogram_project_map_to_streamlines.py
+++ b/scripts/tests/test_tractogram_project_map_to_streamlines.py
@@ -19,12 +19,12 @@ def test_help_option(script_runner):
 
 def test_execution_3D_map(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
-    in_fa = os.path.join(get_home(), 'others', 'fa.nii.gz')
+    in_t1 = os.path.join(get_home(), 'tractometry', 'mni_masked.nii.gz')
     in_tracto_1 = os.path.join(get_home(), 'others',
                                'IFGWM_sub.trk')
 
     ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
-                            in_tracto_1, in_fa, 'fa_on_streamlines.trk')
+                            in_tracto_1, in_t1, 't1_on_streamlines.trk')
     assert ret.success
 
 
@@ -41,12 +41,12 @@ def test_execution_4D_map(script_runner):
 
 def test_execution_3D_map_endpoints_only(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
-    in_fa = os.path.join(get_home(), 'others', 'fa.nii.gz')
+    in_t1 = os.path.join(get_home(), 'tractometry', 'mni_masked.nii.gz')
     in_tracto_1 = os.path.join(get_home(), 'others',
                                'IFGWM_sub.trk')
 
     ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
-                            in_tracto_1, in_fa, 'fa_on_streamlines.trk',
+                            in_tracto_1, in_t1, 't1_on_streamlines_endpoints.trk',
                             '--endpoints_only')
     assert ret.success
 
@@ -58,30 +58,30 @@ def test_execution_4D_map_endpoints_only(script_runner):
                                'IFGWM_sub.trk')
 
     ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
-                            in_tracto_1, in_rgb, 'rgb_on_streamlines.trk',
+                            in_tracto_1, in_rgb, 'rgb_on_streamlines_endpoints.trk',
                             '--endpoints_only')
     assert ret.success
 
 
 def test_execution_3D_map_dpp_name(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
-    in_fa = os.path.join(get_home(), 'others', 'fa.nii.gz')
+    in_t1 = os.path.join(get_home(), 'tractometry', 'mni_masked.nii.gz')
     in_tracto_1 = os.path.join(get_home(), 'others',
                                'IFGWM_sub.trk')
 
     ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
-                            in_tracto_1, in_fa, 'fa_on_streamlines.trk',
-                            '--dpp_name', 'fa')
+                            in_tracto_1, in_t1, 't1_on_streamlines_dpp_name.trk',
+                            '--dpp_name', 't1')
     assert ret.success
 
 
 def test_execution_3D_map_trilinear(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
-    in_fa = os.path.join(get_home(), 'others', 'fa.nii.gz')
+    in_t1 = os.path.join(get_home(), 'tractometry', 'mni_masked.nii.gz')
     in_tracto_1 = os.path.join(get_home(), 'others',
                                'IFGWM_sub.trk')
 
     ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
-                            in_tracto_1, in_fa, 'fa_on_streamlines.trk',
+                            in_tracto_1, in_t1, 't1_on_streamlines_trilinear.trk',
                             '--trilinear')
     assert ret.success

From dded388d1b0474d9d08673dcfbb1cf185189b84a Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 15 Jan 2024 12:05:29 -0500
Subject: [PATCH 26/97] added test for point math

---
 scripts/tests/test_tractogram_point_math.py | 35 +++++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 scripts/tests/test_tractogram_point_math.py

diff --git a/scripts/tests/test_tractogram_point_math.py b/scripts/tests/test_tractogram_point_math.py
new file mode 100644
index 000000000..db240cceb
--- /dev/null
+++ b/scripts/tests/test_tractogram_point_math.py
@@ -0,0 +1,35 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import os
+import tempfile
+
+from scilpy.io.fetcher import get_testing_files_dict, fetch_data, get_home
+
+
+# If they already exist, this only takes 5 seconds (check md5sum)
+fetch_data(get_testing_files_dict(), keys=['tractometry.zip'])
+tmp_dir = tempfile.TemporaryDirectory()
+
+
+def test_help_option(script_runner):
+    ret = script_runner.run('scil_tractogram_point_math.py', '--help')
+    assert ret.success
+
+
+def test_execution_tractogram_point_math_mean_3D_defaults(script_runner):
+    os.chdir(os.path.expanduser(tmp_dir.name))
+    in_bundle = os.path.join(get_home(), 'tractometry',
+                             'IFGWM_uni.trk')
+    in_t1 = os.path.join(get_home(), 'tractometry',
+                         'mni_masked.nii.gz')
+
+    t1_on_bundle = 't1_on_streamlines.trk'
+
+    script_runner.run('scil_tractogram_project_map_to_streamlines.py',
+                      in_bundle, in_t1, t1_on_bundle)
+
+    ret = script_runner.run('scil_tractogram_point_math.py', 'mean', t1_on_bundle,
+                            't1_mean_on_streamlines.trk')
+
+    assert ret.success

From 7592d60fd7ceb7255d10e8713ac0ad510569a196 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 15 Jan 2024 12:39:18 -0500
Subject: [PATCH 27/97] changed arg name for point math output

---
 scripts/scil_tractogram_point_math.py | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/scripts/scil_tractogram_point_math.py b/scripts/scil_tractogram_point_math.py
index 7adf7d61a..6a22e6b3b 100755
--- a/scripts/scil_tractogram_point_math.py
+++ b/scripts/scil_tractogram_point_math.py
@@ -74,9 +74,10 @@ def _build_arg_parser():
                    help='Name of the data_per_point for operation to be '
                         'performed on. (Default: %(default)s)')
 
-    p.add_argument('--output_dpp_name', default='metric_math',
-                   help='Name of the resulting data_per_point to be saved \n'
-                   'in the output tractogram. (Default: %(default)s)')
+    p.add_argument('--output_name', default='metric_math',
+                   help='Name of the resulting data_per_point or '
+                   'data_per_streamline to be saved in the output '
+                   'tractogram. (Default: %(default)s)')
 
     add_reference_arg(p)
     add_verbose_arg(p)
@@ -134,7 +135,7 @@ def main():
                                          sft.space_attributes,
                                          sft.space, sft.origin,
                                          data_per_streamline={
-                                             args.output_dpp_name:
+                                             args.output_name:
                                              new_dps})
         else:
             # Results in new data per point
@@ -149,7 +150,7 @@ def main():
                                          sft.space_attributes,
                                          sft.space, sft.origin,
                                          data_per_point={
-                                             args.output_dpp_name:
+                                             args.output_name:
                                              new_dpp})
     else:
         # Results in new data per streamline
@@ -162,7 +163,7 @@ def main():
         new_sft = StatefulTractogram(sft.streamlines, sft.space_attributes,
                                      sft.space, sft.origin,
                                      data_per_streamline={
-                                         args.output_dpp_name:
+                                         args.output_name:
                                          new_data_per_streamline})
 
     if len(new_sft) == 0 and not args.save_empty:

From 8a6973d2a3d1705020eabd860a5e18a14f65e88e Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 15 Jan 2024 13:57:08 -0500
Subject: [PATCH 28/97] pep 8 long lines

---
 scripts/tests/test_tractogram_point_math.py          |  4 +++-
 .../test_tractogram_project_map_to_streamlines.py    | 12 ++++++++----
 2 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/scripts/tests/test_tractogram_point_math.py b/scripts/tests/test_tractogram_point_math.py
index db240cceb..90f1dc135 100644
--- a/scripts/tests/test_tractogram_point_math.py
+++ b/scripts/tests/test_tractogram_point_math.py
@@ -29,7 +29,9 @@ def test_execution_tractogram_point_math_mean_3D_defaults(script_runner):
     script_runner.run('scil_tractogram_project_map_to_streamlines.py',
                       in_bundle, in_t1, t1_on_bundle)
 
-    ret = script_runner.run('scil_tractogram_point_math.py', 'mean', t1_on_bundle,
+    ret = script_runner.run('scil_tractogram_point_math.py',
+                            'mean',
+                            t1_on_bundle,
                             't1_mean_on_streamlines.trk')
 
     assert ret.success
diff --git a/scripts/tests/test_tractogram_project_map_to_streamlines.py b/scripts/tests/test_tractogram_project_map_to_streamlines.py
index 13dcf4fcb..83adef48f 100644
--- a/scripts/tests/test_tractogram_project_map_to_streamlines.py
+++ b/scripts/tests/test_tractogram_project_map_to_streamlines.py
@@ -46,7 +46,8 @@ def test_execution_3D_map_endpoints_only(script_runner):
                                'IFGWM_sub.trk')
 
     ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
-                            in_tracto_1, in_t1, 't1_on_streamlines_endpoints.trk',
+                            in_tracto_1, in_t1,
+                            't1_on_streamlines_endpoints.trk',
                             '--endpoints_only')
     assert ret.success
 
@@ -58,7 +59,8 @@ def test_execution_4D_map_endpoints_only(script_runner):
                                'IFGWM_sub.trk')
 
     ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
-                            in_tracto_1, in_rgb, 'rgb_on_streamlines_endpoints.trk',
+                            in_tracto_1, in_rgb,
+                            'rgb_on_streamlines_endpoints.trk',
                             '--endpoints_only')
     assert ret.success
 
@@ -70,7 +72,8 @@ def test_execution_3D_map_dpp_name(script_runner):
                                'IFGWM_sub.trk')
 
     ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
-                            in_tracto_1, in_t1, 't1_on_streamlines_dpp_name.trk',
+                            in_tracto_1, in_t1,
+                            't1_on_streamlines_dpp_name.trk',
                             '--dpp_name', 't1')
     assert ret.success
 
@@ -82,6 +85,7 @@ def test_execution_3D_map_trilinear(script_runner):
                                'IFGWM_sub.trk')
 
     ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
-                            in_tracto_1, in_t1, 't1_on_streamlines_trilinear.trk',
+                            in_tracto_1, in_t1,
+                            't1_on_streamlines_trilinear.trk',
                             '--trilinear')
     assert ret.success

From 62c103c48b85699777a3749609fdf8df44eec836 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 15 Jan 2024 15:16:45 -0500
Subject: [PATCH 29/97] updated function names in stream_ops

---
 scilpy/tractograms/streamline_operations.py | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/scilpy/tractograms/streamline_operations.py b/scilpy/tractograms/streamline_operations.py
index 20d8be343..fe727426d 100644
--- a/scilpy/tractograms/streamline_operations.py
+++ b/scilpy/tractograms/streamline_operations.py
@@ -499,32 +499,32 @@ def perform_streamline_operation_on_endpoints(op_name, sft, dpp_name='metric'):
     return new_data_per_streamline
 
 
-def mean(array):
+def stream_mean(array):
     return np.mean(array)
 
 
-def sum(array):
+def stream_sum(array):
     return np.sum(array)
 
 
-def min(array):
+def stream_min(array):
     return np.min(array)
 
 
-def max(array):
+def stream_max(array):
     return np.max(array)
 
 
-def correlation(array1, array2):
+def stream_correlation(array1, array2):
     return np.corrcoef(array1, array2)
 
 
 OPERATIONS = {
-    'mean': mean,
-    'sum': sum,
-    'min': min,
-    'max': max,
-    'correlation': correlation,
+    'mean': stream_mean,
+    'sum': stream_sum,
+    'min': stream_min,
+    'max': stream_max,
+    'correlation': stream_correlation,
 }
 
 

From ffc2c88e07e7c4f4027a35a2a6df890f49fa15e2 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Thu, 25 Jan 2024 12:56:08 -0500
Subject: [PATCH 30/97] Fixed for loops and added multi input

---
 scilpy/tractograms/streamline_operations.py   |  14 +-
 scripts/scil_tractogram_point_math.py         | 128 +++++++++---------
 ...l_tractogram_project_map_to_streamlines.py |  72 +++++-----
 scripts/tests/.python-version                 |   1 +
 4 files changed, 111 insertions(+), 104 deletions(-)
 create mode 100644 scripts/tests/.python-version

diff --git a/scilpy/tractograms/streamline_operations.py b/scilpy/tractograms/streamline_operations.py
index fe727426d..becc00029 100644
--- a/scilpy/tractograms/streamline_operations.py
+++ b/scilpy/tractograms/streamline_operations.py
@@ -417,9 +417,7 @@ def perform_streamline_operation_per_point(op_name, sft, dpp_name='metric',
     if endpoints_only:
         new_data_per_point = []
         for s in sft.data_per_point[dpp_name]:
-            this_data_per_point = []
-            for p in s:
-                this_data_per_point.append(np.asarray(0.))
+            this_data_per_point = np.nan * np.ones((len(s), 1))
             this_data_per_point[0] = call_op(s[0])
             this_data_per_point[-1] = call_op(s[-1])
             new_data_per_point.append(
@@ -566,12 +564,10 @@ def project_metric_to_streamlines(sft, metric, endpoints_only=False):
                 s[-1][0], s[-1][1], s[-1][2],
                 space=sft.space, origin=sft.origin)
             thisstreamline_data = []
-            for p in s:
-                if dimension == 1:
-                    thisstreamline_data.append(0)
-                else:
-                    thisstreamline_data.append(
-                        np.asarray(np.repeat(0, p1_data.shape[0])))
+            if dimension == 1:
+                thisstreamline_data = np.ones((len(s), 1)) * np.nan
+            else:
+                thisstreamline_data = np.ones((len(s), p1_data.shape[0])) * np.nan
 
             thisstreamline_data[0] = p1_data
             thisstreamline_data[-1] = p2_data
diff --git a/scripts/scil_tractogram_point_math.py b/scripts/scil_tractogram_point_math.py
index 6a22e6b3b..a7f1b3abe 100755
--- a/scripts/scil_tractogram_point_math.py
+++ b/scripts/scil_tractogram_point_math.py
@@ -62,6 +62,15 @@ def _build_arg_parser():
     p.add_argument('in_tractogram', metavar='INPUT_FILE',
                    help='Input tractogram containing streamlines and '
                         'metadata.')
+    p.add_argument('--in_dpp_name',  nargs='+', action='append',
+                   required=True,
+                   help='Name of the data_per_point for operation to be '
+                        'performed on.')
+    p.add_argument('--out_name', nargs='+', action='append',
+                   required=True,
+                   help='Name of the resulting data_per_point or '
+                   'data_per_streamline to be saved in the output '
+                   'tractogram. (Default: %(default)s)')
     p.add_argument('out_tractogram', metavar='OUTPUT_FILE',
                    help='The file where the remaining streamlines '
                         'are saved.')
@@ -70,14 +79,7 @@ def _build_arg_parser():
                    help='If set, will only perform operation on endpoints \n'
                    'If not set, will perform operation on all streamline \n'
                    'points.')
-    p.add_argument('--dpp_name', default='metric',
-                   help='Name of the data_per_point for operation to be '
-                        'performed on. (Default: %(default)s)')
 
-    p.add_argument('--output_name', default='metric_math',
-                   help='Name of the resulting data_per_point or '
-                   'data_per_streamline to be saved in the output '
-                   'tractogram. (Default: %(default)s)')
 
     add_reference_arg(p)
     add_verbose_arg(p)
@@ -105,66 +107,66 @@ def main():
         logging.info("Input tractogram contains no streamlines. Exiting.")
         return
 
-    # Check to see if the data per point exists.
-    if args.dpp_name not in sft.data_per_point:
-        logging.info('Data per point {} not found in input tractogram.'
-                     .format(args.dpp_name))
-        return
-
-    # check size of first streamline data_per_point
-    if sft.data_per_point[args.dpp_name][0].shape[1] == 1:
-        is_singular = True
-    else:
-        is_singular = False
-
-    if args.operation == 'correlation' and is_singular:
-        logging.info('Correlation operation requires multivalued data per '
-                     'point. Exiting.')
-        return
+    if len(args.in_dpp_name[0]) != len(args.out_name[0]):
+        parser.error('The number of in_dpp_names and out_names must be '
+                     'the same.')
+
+    data_per_point = {}
+    data_per_streamline = {}
+    for in_dpp_name, out_name in zip(args.in_dpp_name[0],
+                                           args.out_name[0]):
+        # Check to see if the data per point exists.
+        if in_dpp_name not in sft.data_per_point:
+            logging.info('Data per point {} not found in input tractogram.'
+                        .format(in_dpp_name))
+            return
+
+        # check size of first streamline data_per_point
+        if sft.data_per_point[in_dpp_name][0].shape[1] == 1:
+            is_singular = True
+        else:
+            is_singular = False
 
-    # Perform the requested operation.
-    if not is_singular:
-        if args.operation == 'correlation':
-            logging.info('Performing {} across endpoint data.'.format(
-                args.operation))
-            new_dps = perform_streamline_operation_on_endpoints(
-                args.operation, sft, args.dpp_name)
+        if args.operation == 'correlation' and is_singular:
+            logging.info('Correlation operation requires multivalued data per '
+                        'point. Exiting.')
+            return
 
-            # Adding data per streamline to new_sft
-            new_sft = StatefulTractogram(sft.streamlines,
-                                         sft.space_attributes,
-                                         sft.space, sft.origin,
-                                         data_per_streamline={
-                                             args.output_name:
-                                             new_dps})
+        # Perform the requested operation.
+        if not is_singular:
+            if args.operation == 'correlation':
+                logging.info('Performing {} across endpoint data.'.format(
+                    args.operation))
+                new_dps = perform_streamline_operation_on_endpoints(
+                    args.operation, sft, in_dpp_name)
+
+                # Adding data per streamline to new_sft
+                data_per_streamline[out_name] = new_dps
+            else:
+                # Results in new data per point
+                logging.info(
+                    'Performing {} on data from each streamine point.'.format(
+                        args.operation))
+                new_dpp = perform_streamline_operation_per_point(
+                    args.operation, sft, in_dpp_name, args.endpoints_only)
+
+                # Adding data per point to new_sft
+                data_per_point[out_name] = new_dpp
         else:
-            # Results in new data per point
+            # Results in new data per streamline
             logging.info(
-                'Performing {} on data from each streamine point.'.format(
-                    args.operation))
-            new_dpp = perform_streamline_operation_per_point(
-                args.operation, sft, args.dpp_name, args.endpoints_only)
-
-            # Adding data per point to new_sft
-            new_sft = StatefulTractogram(sft.streamlines,
-                                         sft.space_attributes,
-                                         sft.space, sft.origin,
-                                         data_per_point={
-                                             args.output_name:
-                                             new_dpp})
-    else:
-        # Results in new data per streamline
-        logging.info(
-            'Performing {} across each streamline.'.format(args.operation))
-        new_data_per_streamline = perform_operation_per_streamline(
-            args.operation, sft, args.dpp_name, args.endpoints_only)
-
-        # Adding data per streamline to new_sft
-        new_sft = StatefulTractogram(sft.streamlines, sft.space_attributes,
-                                     sft.space, sft.origin,
-                                     data_per_streamline={
-                                         args.output_name:
-                                         new_data_per_streamline})
+                'Performing {} across each streamline.'.format(args.operation))
+            new_data_per_streamline = perform_operation_per_streamline(
+                args.operation, sft, in_dpp_name, args.endpoints_only)
+
+            # Adding data per streamline to new_sft
+            data_per_streamline[out_name] = new_data_per_streamline
+
+    new_sft = StatefulTractogram(sft.streamlines,
+                                 sft.space_attributes,
+                                 sft.space, sft.origin,
+                                 data_per_point=data_per_point,
+                                 data_per_streamline=data_per_streamline)
 
     if len(new_sft) == 0 and not args.save_empty:
         logging.info("Empty resulting tractogram. Not saving results.")
diff --git a/scripts/scil_tractogram_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
index 34ef2152c..ef001c9c6 100755
--- a/scripts/scil_tractogram_project_map_to_streamlines.py
+++ b/scripts/scil_tractogram_project_map_to_streamlines.py
@@ -11,20 +11,18 @@
 import argparse
 import logging
 
+from dipy.io.streamline import save_tractogram, StatefulTractogram
+
 from scilpy.io.image import load_img
 from scilpy.io.streamlines import load_tractogram_with_reference
-from scilpy.tractograms.streamline_operations import (
-    project_metric_to_streamlines)
 from scilpy.io.utils import (add_overwrite_arg,
-                             assert_inputs_exist,
-                             assert_outputs_exist,
                              add_reference_arg,
-                             add_verbose_arg)
-
+                             add_verbose_arg,
+                             assert_inputs_exist,
+                             assert_outputs_exist)
 from scilpy.image.volume_space_management import DataVolume
-
-from dipy.io.streamline import save_tractogram, StatefulTractogram
-
+from scilpy.tractograms.streamline_operations import (
+    project_metric_to_streamlines)
 
 def _build_arg_parser():
     p = argparse.ArgumentParser(
@@ -34,10 +32,13 @@ def _build_arg_parser():
     # Mandatory arguments input and output tractogram must be in trk format
     p.add_argument('in_tractogram',
                    help='Fiber bundle file.')
-    p.add_argument('in_metric',
-                   help='Nifti metric to project onto streamlines.')
     p.add_argument('out_tractogram',
                    help='Output file.')
+    p.add_argument('--in_metric', nargs='+', action='append', required=True,
+                   help='Nifti metric to project onto streamlines.')
+    p.add_argument('--out_dpp_name', nargs='+', action='append', required=True,
+                   help='Name of the data_per_point to be saved in the \n'
+                   'output tractogram.')
 
     # Optional arguments
     p.add_argument('--trilinear', action='store_true',
@@ -48,12 +49,9 @@ def _build_arg_parser():
     p.add_argument('--endpoints_only', action='store_true',
                    help='If set, will only project the metric onto the \n'
                    'endpoints of the streamlines (all other values along \n'
-                   ' streamlines set to zero). If not set, will project \n'
+                   ' streamlines will be NaN). If not set, will project \n'
                    ' the metric onto all points of the streamlines.')
 
-    p.add_argument('--dpp_name', default='metric',
-                   help='Name of the data_per_point to be saved in the \n'
-                   'output tractogram. (Default: %(default)s)')
     add_reference_arg(p)
     add_overwrite_arg(p)
     add_verbose_arg(p)
@@ -64,7 +62,10 @@ def main():
     parser = _build_arg_parser()
     args = parser.parse_args()
 
-    assert_inputs_exist(parser, [args.in_tractogram, args.in_metric])
+    input_file_list = [args.in_tractogram]
+    for fmetric in args.in_metric:
+        input_file_list += fmetric
+    assert_inputs_exist(parser, input_file_list)
 
     assert_outputs_exist(parser, args, [args.out_tractogram])
 
@@ -77,26 +78,33 @@ def main():
         logging.warning('Empty bundle file {}. Skipping'.format(args.bundle))
         return
 
-    logging.debug("Loading the metric...")
-    metric_img, metric_dtype = load_img(args.in_metric)
-    metric_data = metric_img.get_fdata(caching='unchanged', dtype=float)
-    metric_res = metric_img.header.get_zooms()[:3]
+    # Check to see if the number of metrics and dpp_names are the same
+    if len(args.in_metric) != len(args.out_dpp_name):
+        parser.error('The number of metrics and dpp_names must be the same.')
 
-    if args.trilinear:
-        interp = "trilinear"
-    else:
-        interp = "nearest"
+    data_per_point = {}
+    for fmetric, dpp_name in zip(args.in_metric[0], args.out_dpp_name[0]):
+        logging.debug("Loading the metric...")
+        metric_img, metric_dtype = load_img(fmetric)
+        metric_data = metric_img.get_fdata(caching='unchanged', dtype=float)
+        metric_res = metric_img.header.get_zooms()[:3]
 
-    metric = DataVolume(metric_data, metric_res, interp)
+        if args.trilinear:
+            interp = "trilinear"
+        else:
+            interp = "nearest"
 
-    logging.debug("Projecting metric onto streamlines")
-    streamline_data = project_metric_to_streamlines(
-        sft, metric,
-        endpoints_only=args.endpoints_only)
+        metric = DataVolume(metric_data, metric_res, interp)
+
+        logging.debug("Projecting metric onto streamlines")
+        streamline_data = project_metric_to_streamlines(
+            sft, metric,
+            endpoints_only=args.endpoints_only)
+
+        logging.debug("Saving the tractogram...")
+
+        data_per_point[dpp_name] = streamline_data
 
-    logging.debug("Saving the tractogram...")
-    data_per_point = {}
-    data_per_point[args.dpp_name] = streamline_data
     out_sft = StatefulTractogram(sft.streamlines, metric_img,
                                  sft.space, sft.origin,
                                  data_per_point=data_per_point)
diff --git a/scripts/tests/.python-version b/scripts/tests/.python-version
new file mode 100644
index 000000000..c8cfe3959
--- /dev/null
+++ b/scripts/tests/.python-version
@@ -0,0 +1 @@
+3.10

From 89f40d2f5dbdb219effe42589d066fdc5090f0d3 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Thu, 25 Jan 2024 13:02:38 -0500
Subject: [PATCH 31/97] updated projection tests with new required args

---
 ...t_tractogram_project_map_to_streamlines.py | 34 ++++++++-----------
 1 file changed, 15 insertions(+), 19 deletions(-)

diff --git a/scripts/tests/test_tractogram_project_map_to_streamlines.py b/scripts/tests/test_tractogram_project_map_to_streamlines.py
index 83adef48f..2ed5b9b56 100644
--- a/scripts/tests/test_tractogram_project_map_to_streamlines.py
+++ b/scripts/tests/test_tractogram_project_map_to_streamlines.py
@@ -24,7 +24,9 @@ def test_execution_3D_map(script_runner):
                                'IFGWM_sub.trk')
 
     ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
-                            in_tracto_1, in_t1, 't1_on_streamlines.trk')
+                            in_tracto_1, 't1_on_streamlines.trk',
+                            '--in_metric', in_t1,
+                            '--out_dpp_name', 't1')
     assert ret.success
 
 
@@ -35,7 +37,9 @@ def test_execution_4D_map(script_runner):
                                'IFGWM_sub.trk')
 
     ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
-                            in_tracto_1, in_rgb, 'rgb_on_streamlines.trk')
+                            in_tracto_1, 'rgb_on_streamlines.trk',
+                            '--in_metric', in_rgb,
+                            '--out_dpp_name', 'rgb')
     assert ret.success
 
 
@@ -46,8 +50,10 @@ def test_execution_3D_map_endpoints_only(script_runner):
                                'IFGWM_sub.trk')
 
     ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
-                            in_tracto_1, in_t1,
+                            in_tracto_1,
                             't1_on_streamlines_endpoints.trk',
+                            '--in_metric', in_t1,
+                            '--out_dpp_name', 't1',
                             '--endpoints_only')
     assert ret.success
 
@@ -59,25 +65,13 @@ def test_execution_4D_map_endpoints_only(script_runner):
                                'IFGWM_sub.trk')
 
     ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
-                            in_tracto_1, in_rgb,
+                            in_tracto_1,
                             'rgb_on_streamlines_endpoints.trk',
+                            '--in_metric', in_rgb,
+                            '--out_dpp_name', 'rgb',
                             '--endpoints_only')
     assert ret.success
 
-
-def test_execution_3D_map_dpp_name(script_runner):
-    os.chdir(os.path.expanduser(tmp_dir.name))
-    in_t1 = os.path.join(get_home(), 'tractometry', 'mni_masked.nii.gz')
-    in_tracto_1 = os.path.join(get_home(), 'others',
-                               'IFGWM_sub.trk')
-
-    ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
-                            in_tracto_1, in_t1,
-                            't1_on_streamlines_dpp_name.trk',
-                            '--dpp_name', 't1')
-    assert ret.success
-
-
 def test_execution_3D_map_trilinear(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_t1 = os.path.join(get_home(), 'tractometry', 'mni_masked.nii.gz')
@@ -85,7 +79,9 @@ def test_execution_3D_map_trilinear(script_runner):
                                'IFGWM_sub.trk')
 
     ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
-                            in_tracto_1, in_t1,
+                            in_tracto_1,
                             't1_on_streamlines_trilinear.trk',
+                            '--in_metric', in_t1,
+                            '--out_dpp_name', 't1',
                             '--trilinear')
     assert ret.success

From e8bcaddfec51c92a8566f4d0c338a5c1f3c9e7a7 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Thu, 25 Jan 2024 13:28:16 -0500
Subject: [PATCH 32/97] updated point math test with req args

---
 scripts/tests/test_tractogram_point_math.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/scripts/tests/test_tractogram_point_math.py b/scripts/tests/test_tractogram_point_math.py
index 90f1dc135..fa1b871da 100644
--- a/scripts/tests/test_tractogram_point_math.py
+++ b/scripts/tests/test_tractogram_point_math.py
@@ -27,11 +27,15 @@ def test_execution_tractogram_point_math_mean_3D_defaults(script_runner):
     t1_on_bundle = 't1_on_streamlines.trk'
 
     script_runner.run('scil_tractogram_project_map_to_streamlines.py',
-                      in_bundle, in_t1, t1_on_bundle)
+                      in_bundle, t1_on_bundle,
+                      '--in_metric', in_t1,
+                      '--out_dpp_name', 't1')
 
     ret = script_runner.run('scil_tractogram_point_math.py',
                             'mean',
                             t1_on_bundle,
-                            't1_mean_on_streamlines.trk')
+                            't1_mean_on_streamlines.trk',
+                            '--in_dpp_name', 't1',
+                            '--out_name', 't1_mean')
 
     assert ret.success

From 212975bb36d2b02e85d08e6d41a77d1bb3db19c8 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Thu, 25 Jan 2024 15:25:00 -0500
Subject: [PATCH 33/97] added test for point math correlation

---
 scripts/tests/test_tractogram_point_math.py | 25 +++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/scripts/tests/test_tractogram_point_math.py b/scripts/tests/test_tractogram_point_math.py
index fa1b871da..fdf049a51 100644
--- a/scripts/tests/test_tractogram_point_math.py
+++ b/scripts/tests/test_tractogram_point_math.py
@@ -9,6 +9,7 @@
 
 # If they already exist, this only takes 5 seconds (check md5sum)
 fetch_data(get_testing_files_dict(), keys=['tractometry.zip'])
+fetch_data(get_testing_files_dict(), keys=['tracking.zip'])
 tmp_dir = tempfile.TemporaryDirectory()
 
 
@@ -39,3 +40,27 @@ def test_execution_tractogram_point_math_mean_3D_defaults(script_runner):
                             '--out_name', 't1_mean')
 
     assert ret.success
+
+
+def test_execution_tractogram_point_math_mean_4D_correlation(script_runner):
+    os.chdir(os.path.expanduser(tmp_dir.name))
+    in_bundle = os.path.join(get_home(), 'tracking',
+                             'local_split_0.trk')
+
+    in_fodf = os.path.join(get_home(), 'tracking',
+                          'fodf.nii.gz')
+    fodf_on_bundle = 'fodf_on_streamlines.trk'
+
+    script_runner.run('scil_tractogram_project_map_to_streamlines.py',
+                      in_bundle, fodf_on_bundle,
+                      '--in_metric', in_fodf, in_fodf,
+                      '--out_dpp_name', 'fodf', 'fodf2')
+
+    ret = script_runner.run('scil_tractogram_point_math.py',
+                            'correlation',
+                            fodf_on_bundle,
+                            'fodf_correlation_on_streamlines.trk',
+                            '--in_dpp_name', 'fodf',
+                            '--out_name', 'fodf_correlation')
+
+    assert ret.success

From bdcf75079ea16353c16217f3bc599577efb82035 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Fri, 26 Jan 2024 09:31:04 -0500
Subject: [PATCH 34/97] pep8 fix

---
 scilpy/tractograms/streamline_operations.py                | 3 ++-
 scripts/scil_tractogram_point_math.py                      | 7 +++----
 scripts/scil_tractogram_project_map_to_streamlines.py      | 1 +
 scripts/tests/test_tractogram_point_math.py                | 2 +-
 .../tests/test_tractogram_project_map_to_streamlines.py    | 1 +
 5 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/scilpy/tractograms/streamline_operations.py b/scilpy/tractograms/streamline_operations.py
index becc00029..750531224 100644
--- a/scilpy/tractograms/streamline_operations.py
+++ b/scilpy/tractograms/streamline_operations.py
@@ -567,7 +567,8 @@ def project_metric_to_streamlines(sft, metric, endpoints_only=False):
             if dimension == 1:
                 thisstreamline_data = np.ones((len(s), 1)) * np.nan
             else:
-                thisstreamline_data = np.ones((len(s), p1_data.shape[0])) * np.nan
+                thisstreamline_data = np.ones(
+                    (len(s), p1_data.shape[0])) * np.nan
 
             thisstreamline_data[0] = p1_data
             thisstreamline_data[-1] = p2_data
diff --git a/scripts/scil_tractogram_point_math.py b/scripts/scil_tractogram_point_math.py
index a7f1b3abe..1862e3a4c 100755
--- a/scripts/scil_tractogram_point_math.py
+++ b/scripts/scil_tractogram_point_math.py
@@ -80,7 +80,6 @@ def _build_arg_parser():
                    'If not set, will perform operation on all streamline \n'
                    'points.')
 
-
     add_reference_arg(p)
     add_verbose_arg(p)
     add_overwrite_arg(p)
@@ -114,11 +113,11 @@ def main():
     data_per_point = {}
     data_per_streamline = {}
     for in_dpp_name, out_name in zip(args.in_dpp_name[0],
-                                           args.out_name[0]):
+                                     args.out_name[0]):
         # Check to see if the data per point exists.
         if in_dpp_name not in sft.data_per_point:
             logging.info('Data per point {} not found in input tractogram.'
-                        .format(in_dpp_name))
+                         .format(in_dpp_name))
             return
 
         # check size of first streamline data_per_point
@@ -129,7 +128,7 @@ def main():
 
         if args.operation == 'correlation' and is_singular:
             logging.info('Correlation operation requires multivalued data per '
-                        'point. Exiting.')
+                         'point. Exiting.')
             return
 
         # Perform the requested operation.
diff --git a/scripts/scil_tractogram_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
index ef001c9c6..89a113201 100755
--- a/scripts/scil_tractogram_project_map_to_streamlines.py
+++ b/scripts/scil_tractogram_project_map_to_streamlines.py
@@ -24,6 +24,7 @@
 from scilpy.tractograms.streamline_operations import (
     project_metric_to_streamlines)
 
+
 def _build_arg_parser():
     p = argparse.ArgumentParser(
         description=__doc__,
diff --git a/scripts/tests/test_tractogram_point_math.py b/scripts/tests/test_tractogram_point_math.py
index fdf049a51..99ab6c966 100644
--- a/scripts/tests/test_tractogram_point_math.py
+++ b/scripts/tests/test_tractogram_point_math.py
@@ -48,7 +48,7 @@ def test_execution_tractogram_point_math_mean_4D_correlation(script_runner):
                              'local_split_0.trk')
 
     in_fodf = os.path.join(get_home(), 'tracking',
-                          'fodf.nii.gz')
+                           'fodf.nii.gz')
     fodf_on_bundle = 'fodf_on_streamlines.trk'
 
     script_runner.run('scil_tractogram_project_map_to_streamlines.py',
diff --git a/scripts/tests/test_tractogram_project_map_to_streamlines.py b/scripts/tests/test_tractogram_project_map_to_streamlines.py
index 2ed5b9b56..c4b171490 100644
--- a/scripts/tests/test_tractogram_project_map_to_streamlines.py
+++ b/scripts/tests/test_tractogram_project_map_to_streamlines.py
@@ -72,6 +72,7 @@ def test_execution_4D_map_endpoints_only(script_runner):
                             '--endpoints_only')
     assert ret.success
 
+
 def test_execution_3D_map_trilinear(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_t1 = os.path.join(get_home(), 'tractometry', 'mni_masked.nii.gz')

From 4c2d8448618499bb73e9d6ac8fd4b359838d0f51 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <graham.little.phd@gmail.com>
Date: Mon, 29 Jan 2024 11:53:47 -0500
Subject: [PATCH 35/97] Updated doc and logging in point_math

---
 scripts/scil_tractogram_point_math.py | 46 +++++++++++++--------------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/scripts/scil_tractogram_point_math.py b/scripts/scil_tractogram_point_math.py
index 1862e3a4c..b5e6fa485 100755
--- a/scripts/scil_tractogram_point_math.py
+++ b/scripts/scil_tractogram_point_math.py
@@ -6,23 +6,24 @@
 resulting in data per streamline.  The supported
 operations are:
 
-If the input is singular per point then:
+If the chosen dpp key refers to numerical values (one single number per point):
 mean: mean across points per streamline
 sum: sum across points per streamline
 min: min value across points per streamline
 max: max value across points per streamline
 
-endpoints_only is set, min/max/mean/sum will only
+if endpoints_only is set, min/max/mean/sum will only
 be calculated using the streamline endpoints
 
-If the input is multivalued per point then:
+If the chosen dpp key refers to data stored as arrays (multiple numbers per point):
 mean: mean calculated per point for each streamline
 sum: sum calculated per point for each streamline
 min: min value calculated per point for each streamline
 max: max value calculated per point for each streamline
 
-endpoints_only is set, min/max/mean/sum will only
-be calculated at the streamline endpoints
+if endpoints_only is set, min/max/mean/sum will only
+be calculated at the streamline endpoints the rest of the
+values along the streamline will be NaN
 
 Endpoint only operations:
 correlation: correlation calculated between arrays extracted from
@@ -41,7 +42,6 @@
                              add_verbose_arg,
                              assert_inputs_exist,
                              assert_outputs_exist)
-
 from scilpy.tractograms.streamline_operations import (
         perform_streamline_operation_on_endpoints,
         perform_streamline_operation_per_point,
@@ -64,13 +64,16 @@ def _build_arg_parser():
                         'metadata.')
     p.add_argument('--in_dpp_name',  nargs='+', action='append',
                    required=True,
-                   help='Name of the data_per_point for operation to be '
-                        'performed on.')
+                   help='Name or list of names of the data_per_point for '
+                        'operation to be performed on. If more than one dpp '
+                        'is selected, the same operation will be applied '
+                        'separately to each one.')
     p.add_argument('--out_name', nargs='+', action='append',
                    required=True,
                    help='Name of the resulting data_per_point or '
                    'data_per_streamline to be saved in the output '
-                   'tractogram. (Default: %(default)s)')
+                   'tractogram. If more than one --in_dpp_name was used, '
+                   'enter the same number of --out_name values.')
     p.add_argument('out_tractogram', metavar='OUTPUT_FILE',
                    help='The file where the remaining streamlines '
                         'are saved.')
@@ -110,6 +113,10 @@ def main():
         parser.error('The number of in_dpp_names and out_names must be '
                      'the same.')
 
+    # Check to see if there are duplicates in the out_names
+    if len(args.out_name[0]) != len(set(args.out_name[0])):
+        parser.error('The output names (out_names) must be unique.')
+
     data_per_point = {}
     data_per_streamline = {}
     for in_dpp_name, out_name in zip(args.in_dpp_name[0],
@@ -134,31 +141,28 @@ def main():
         # Perform the requested operation.
         if not is_singular:
             if args.operation == 'correlation':
-                logging.info('Performing {} across endpoint data.'.format(
-                    args.operation))
+                logging.info('Performing {} across endpoint data and saving as new dpp {}'.format(
+                    args.operation, out_name))
                 new_dps = perform_streamline_operation_on_endpoints(
                     args.operation, sft, in_dpp_name)
 
-                # Adding data per streamline to new_sft
                 data_per_streamline[out_name] = new_dps
             else:
                 # Results in new data per point
                 logging.info(
-                    'Performing {} on data from each streamine point.'.format(
-                        args.operation))
+                    'Performing {} on data from each streamine point '
+                    'and saving as new dpp {}'.format(
+                        args.operation, out_name))
                 new_dpp = perform_streamline_operation_per_point(
                     args.operation, sft, in_dpp_name, args.endpoints_only)
-
-                # Adding data per point to new_sft
                 data_per_point[out_name] = new_dpp
         else:
             # Results in new data per streamline
             logging.info(
-                'Performing {} across each streamline.'.format(args.operation))
+                'Performing {} across each streamline and saving resulting '
+                'data per streamline {}'.format(args.operation, out_name))
             new_data_per_streamline = perform_operation_per_streamline(
                 args.operation, sft, in_dpp_name, args.endpoints_only)
-
-            # Adding data per streamline to new_sft
             data_per_streamline[out_name] = new_data_per_streamline
 
     new_sft = StatefulTractogram(sft.streamlines,
@@ -167,10 +171,6 @@ def main():
                                  data_per_point=data_per_point,
                                  data_per_streamline=data_per_streamline)
 
-    if len(new_sft) == 0 and not args.save_empty:
-        logging.info("Empty resulting tractogram. Not saving results.")
-        return
-
     # Save the new streamlines (and metadata)
     logging.info('Saving {} streamlines to {}.'.format(len(new_sft),
                                                        args.out_tractogram))

From 67873b99dbb210ff2bdcd1971b23c0f196fe9923 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 29 Jan 2024 15:15:48 -0500
Subject: [PATCH 36/97] added dpp and dpp mode argument

---
 scilpy/tractograms/streamline_operations.py |  11 +-
 scripts/scil_tractogram_point_math.py       | 109 +++++++++++---------
 2 files changed, 65 insertions(+), 55 deletions(-)

diff --git a/scilpy/tractograms/streamline_operations.py b/scilpy/tractograms/streamline_operations.py
index 750531224..8e053fe08 100644
--- a/scilpy/tractograms/streamline_operations.py
+++ b/scilpy/tractograms/streamline_operations.py
@@ -437,7 +437,7 @@ def perform_streamline_operation_per_point(op_name, sft, dpp_name='metric',
 
 def perform_operation_per_streamline(op_name, sft, dpp_name='metric',
                                      endpoints_only=False):
-    """Peforms an operation across points for each streamline.
+    """Performs an operation across all data points for each streamline.
 
     Parameters
     ----------
@@ -461,16 +461,19 @@ def perform_operation_per_streamline(op_name, sft, dpp_name='metric',
     if endpoints_only:
         new_data_per_streamline = []
         for s in sft.data_per_point[dpp_name]:
-            new_data_per_streamline.append(call_op([s[0], s[-1]]))
+            start = s[0]
+            end = s[-1]
+            concat = np.concatenate((start[:], end[:]), axis=0)
+            new_data_per_streamline.append(call_op(concat))
     else:
         new_data_per_streamline = []
         for s in sft.data_per_point[dpp_name]:
-            new_data_per_streamline.append(call_op(s))
+            new_data_per_streamline.append(call_op(s[:]))
 
     return new_data_per_streamline
 
 
-def perform_streamline_operation_on_endpoints(op_name, sft, dpp_name='metric'):
+def perform_pairwise_streamline_operation_on_endpoints(op_name, sft, dpp_name='metric'):
     """Peforms an operation across endpoints for each streamline.
 
     Parameters
diff --git a/scripts/scil_tractogram_point_math.py b/scripts/scil_tractogram_point_math.py
index b5e6fa485..4803e6747 100755
--- a/scripts/scil_tractogram_point_math.py
+++ b/scripts/scil_tractogram_point_math.py
@@ -2,32 +2,29 @@
 # -*- coding: utf-8 -*-
 
 """
-Performs an operation on data per point from streamlines
-resulting in data per streamline.  The supported
-operations are:
-
-If the chosen dpp key refers to numerical values (one single number per point):
-mean: mean across points per streamline
-sum: sum across points per streamline
-min: min value across points per streamline
-max: max value across points per streamline
-
-if endpoints_only is set, min/max/mean/sum will only
-be calculated using the streamline endpoints
-
-If the chosen dpp key refers to data stored as arrays (multiple numbers per point):
-mean: mean calculated per point for each streamline
-sum: sum calculated per point for each streamline
-min: min value calculated per point for each streamline
-max: max value calculated per point for each streamline
-
-if endpoints_only is set, min/max/mean/sum will only
+Performs an operation on data per point from input streamlines.
+
+Two modes of operation are supported: data per streamline (dps) and data per
+point (dpp).
+
+In dps mode, the operation is performed across all dimensions of the data
+resulting in a single value per streamline.
+
+In dpp mode the operation is performed on each point separately, resulting in
+a single value per point.
+
+If endpoints_only and dpp mode is set operation will only
 be calculated at the streamline endpoints the rest of the
 values along the streamline will be NaN
 
-Endpoint only operations:
+If endpoints_only and dps mode is set operation will be calculated
+across the data at the endpoints and stored as a
+single value per streamline.
+
+Endpoint only operation:
 correlation: correlation calculated between arrays extracted from
-streamline endpoints (data must be multivalued per point)
+streamline endpoints (data must be multivalued per point) and dps
+mode must be set.
 """
 
 import argparse
@@ -43,7 +40,7 @@
                              assert_inputs_exist,
                              assert_outputs_exist)
 from scilpy.tractograms.streamline_operations import (
-        perform_streamline_operation_on_endpoints,
+        perform_pairwise_streamline_operation_on_endpoints,
         perform_streamline_operation_per_point,
         perform_operation_per_streamline)
 
@@ -59,6 +56,13 @@ def _build_arg_parser():
                    help='The type of operation to be performed on the '
                         'streamlines. Must\nbe one of the following: '
                         '%(choices)s.')
+    p.add_argument('dpp_or_dps', metavar='DPP_OR_DPS',
+                   choices=['dpp', 'dps'],
+                   help='Set to dps if the operation is to be performed '
+                   'across all dimensions resulting in a single value per '
+                   'streamline. Set to dpp if the operation is to be '
+                   'performed on each point separately resulting in a single '
+                   'value per point.')
     p.add_argument('in_tractogram', metavar='INPUT_FILE',
                    help='Input tractogram containing streamlines and '
                         'metadata.')
@@ -117,46 +121,49 @@ def main():
     if len(args.out_name[0]) != len(set(args.out_name[0])):
         parser.error('The output names (out_names) must be unique.')
 
-    data_per_point = {}
-    data_per_streamline = {}
-    for in_dpp_name, out_name in zip(args.in_dpp_name[0],
-                                     args.out_name[0]):
+    # Input name checks
+    for in_dpp_name in args.in_dpp_name[0]:
         # Check to see if the data per point exists.
         if in_dpp_name not in sft.data_per_point:
             logging.info('Data per point {} not found in input tractogram.'
                          .format(in_dpp_name))
             return
 
-        # check size of first streamline data_per_point
-        if sft.data_per_point[in_dpp_name][0].shape[1] == 1:
-            is_singular = True
-        else:
-            is_singular = False
-
-        if args.operation == 'correlation' and is_singular:
+        data_shape = sft.data_per_point[in_dpp_name][0].shape
+        if args.operation == 'correlation' and len(data_shape) == 1:
             logging.info('Correlation operation requires multivalued data per '
                          'point. Exiting.')
             return
 
+        if args.operation == 'correlation' and args.dpp_or_dps == 'dpp':
+            logging.info('Correlation operation requires dps mode. Exiting.')
+            return
+
+    data_per_point = {}
+    data_per_streamline = {}
+    for in_dpp_name, out_name in zip(args.in_dpp_name[0],
+                                     args.out_name[0]):
+
+
         # Perform the requested operation.
-        if not is_singular:
-            if args.operation == 'correlation':
-                logging.info('Performing {} across endpoint data and saving as new dpp {}'.format(
+        if args.operation == 'correlation':
+            logging.info('Performing {} across endpoint data and saving as '
+                         'new dpp {}'.format(
+                args.operation, out_name))
+            new_dps = perform_pairwise_streamline_operation_on_endpoints(
+                args.operation, sft, in_dpp_name)
+
+            data_per_streamline[out_name] = new_dps
+        elif args.dpp_or_dps == 'dpp':
+            # Results in new data per point
+            logging.info(
+                'Performing {} on data from each streamine point '
+                'and saving as new dpp {}'.format(
                     args.operation, out_name))
-                new_dps = perform_streamline_operation_on_endpoints(
-                    args.operation, sft, in_dpp_name)
-
-                data_per_streamline[out_name] = new_dps
-            else:
-                # Results in new data per point
-                logging.info(
-                    'Performing {} on data from each streamine point '
-                    'and saving as new dpp {}'.format(
-                        args.operation, out_name))
-                new_dpp = perform_streamline_operation_per_point(
-                    args.operation, sft, in_dpp_name, args.endpoints_only)
-                data_per_point[out_name] = new_dpp
-        else:
+            new_dpp = perform_streamline_operation_per_point(
+                args.operation, sft, in_dpp_name, args.endpoints_only)
+            data_per_point[out_name] = new_dpp
+        elif args.dpp_or_dps == 'dps':
             # Results in new data per streamline
             logging.info(
                 'Performing {} across each streamline and saving resulting '

From 154f8ed0ea41f26d68f25cb36dc1ab6a3e8cb2f8 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 29 Jan 2024 16:17:35 -0500
Subject: [PATCH 37/97] added overwrite functionality

---
 scripts/scil_tractogram_point_math.py | 53 +++++++++++++++++++++++----
 1 file changed, 46 insertions(+), 7 deletions(-)

diff --git a/scripts/scil_tractogram_point_math.py b/scripts/scil_tractogram_point_math.py
index 4803e6747..85d7fe4e1 100755
--- a/scripts/scil_tractogram_point_math.py
+++ b/scripts/scil_tractogram_point_math.py
@@ -86,7 +86,10 @@ def _build_arg_parser():
                    help='If set, will only perform operation on endpoints \n'
                    'If not set, will perform operation on all streamline \n'
                    'points.')
-
+    p.add_argument('--overwrite_data', action='store_true', default=False,
+                   help='If set, will overwrite the data_per_point or '
+                   'data_per_streamline in the output tractogram, otherwise '
+                   'previous data will be preserved in the output tractogram.')
     add_reference_arg(p)
     add_verbose_arg(p)
     add_overwrite_arg(p)
@@ -139,6 +142,13 @@ def main():
             logging.info('Correlation operation requires dps mode. Exiting.')
             return
 
+        if args.overwrite_data:
+            if in_dpp_name in args.out_name[0]:
+                logging.info('out_name {} already exists in input tractogram. '
+                             'Unset overwrite_data or choose a different '
+                             'out_name. Exiting.'.format(in_dpp_name))
+                return
+
     data_per_point = {}
     data_per_streamline = {}
     for in_dpp_name, out_name in zip(args.in_dpp_name[0],
@@ -172,11 +182,41 @@ def main():
                 args.operation, sft, in_dpp_name, args.endpoints_only)
             data_per_streamline[out_name] = new_data_per_streamline
 
-    new_sft = StatefulTractogram(sft.streamlines,
-                                 sft.space_attributes,
-                                 sft.space, sft.origin,
-                                 data_per_point=data_per_point,
-                                 data_per_streamline=data_per_streamline)
+
+    if args.overwrite_data:
+        new_sft = sft.from_sft(sft.streamlines, sft,
+                               data_per_point=data_per_point,
+                               data_per_streamline=data_per_streamline)
+    else:
+        old_data_per_streamline = {}
+        for key, value in sft.data_per_streamline.items():
+            old_data_per_streamline[key] = value
+
+        old_data_per_point = {}
+        for key, value in sft.data_per_point.items():
+            old_data_per_point[key] = value
+
+        if data_per_point is not None:
+            for key, value in data_per_point.items():
+                old_data_per_point[key] = value
+
+        if data_per_streamline is not None:
+            for key, value in data_per_streamline.items():
+                old_data_per_streamline[key] = value
+
+        new_sft = sft.from_sft(sft.streamlines, sft,
+                               data_per_point=old_data_per_point,
+                               data_per_streamline=old_data_per_streamline)
+
+    # Print DPP names
+    logging.info('New data per point names:')
+    for key in new_sft.data_per_point.keys():
+        logging.info(key)
+
+    # Print DPS names
+    logging.info('New data per streamline names:')
+    for key in new_sft.data_per_streamline.keys():
+        logging.info(key)
 
     # Save the new streamlines (and metadata)
     logging.info('Saving {} streamlines to {}.'.format(len(new_sft),
@@ -184,6 +224,5 @@ def main():
     save_tractogram(new_sft, args.out_tractogram,
                     bbox_valid_check=args.bbox_check)
 
-
 if __name__ == "__main__":
     main()

From e7b5f0be81c177ed6d26107db984a277f18923de Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 29 Jan 2024 20:14:18 -0500
Subject: [PATCH 38/97] simplify overwrite

---
 scripts/scil_tractogram_point_math.py | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/scripts/scil_tractogram_point_math.py b/scripts/scil_tractogram_point_math.py
index 85d7fe4e1..eaf429e94 100755
--- a/scripts/scil_tractogram_point_math.py
+++ b/scripts/scil_tractogram_point_math.py
@@ -188,13 +188,8 @@ def main():
                                data_per_point=data_per_point,
                                data_per_streamline=data_per_streamline)
     else:
-        old_data_per_streamline = {}
-        for key, value in sft.data_per_streamline.items():
-            old_data_per_streamline[key] = value
-
-        old_data_per_point = {}
-        for key, value in sft.data_per_point.items():
-            old_data_per_point[key] = value
+        old_data_per_streamline = sft.data_per_streamline
+        old_data_per_point = sft.data_per_point
 
         if data_per_point is not None:
             for key, value in data_per_point.items():

From 39f65ef17d7d26108d22aa111053d9ae263e89d4 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 29 Jan 2024 20:17:04 -0500
Subject: [PATCH 39/97] remove append option

---
 scripts/scil_tractogram_point_math.py                 | 4 ++--
 scripts/scil_tractogram_project_map_to_streamlines.py | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/scripts/scil_tractogram_point_math.py b/scripts/scil_tractogram_point_math.py
index eaf429e94..e6224fc1e 100755
--- a/scripts/scil_tractogram_point_math.py
+++ b/scripts/scil_tractogram_point_math.py
@@ -66,13 +66,13 @@ def _build_arg_parser():
     p.add_argument('in_tractogram', metavar='INPUT_FILE',
                    help='Input tractogram containing streamlines and '
                         'metadata.')
-    p.add_argument('--in_dpp_name',  nargs='+', action='append',
+    p.add_argument('--in_dpp_name',  nargs='+',
                    required=True,
                    help='Name or list of names of the data_per_point for '
                         'operation to be performed on. If more than one dpp '
                         'is selected, the same operation will be applied '
                         'separately to each one.')
-    p.add_argument('--out_name', nargs='+', action='append',
+    p.add_argument('--out_name', nargs='+',
                    required=True,
                    help='Name of the resulting data_per_point or '
                    'data_per_streamline to be saved in the output '
diff --git a/scripts/scil_tractogram_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
index 89a113201..a7a76ac20 100755
--- a/scripts/scil_tractogram_project_map_to_streamlines.py
+++ b/scripts/scil_tractogram_project_map_to_streamlines.py
@@ -35,9 +35,9 @@ def _build_arg_parser():
                    help='Fiber bundle file.')
     p.add_argument('out_tractogram',
                    help='Output file.')
-    p.add_argument('--in_metric', nargs='+', action='append', required=True,
+    p.add_argument('--in_metric', nargs='+', required=True,
                    help='Nifti metric to project onto streamlines.')
-    p.add_argument('--out_dpp_name', nargs='+', action='append', required=True,
+    p.add_argument('--out_dpp_name', nargs='+', required=True,
                    help='Name of the data_per_point to be saved in the \n'
                    'output tractogram.')
 

From 6b33f7c325fd0c2340c3a30aef887340edbccb7d Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Tue, 30 Jan 2024 13:22:52 -0500
Subject: [PATCH 40/97] arg multiinput just narg+

---
 scripts/scil_tractogram_point_math.py         | 24 +++++-----
 ...l_tractogram_project_map_to_streamlines.py | 47 ++++++++++++++-----
 2 files changed, 46 insertions(+), 25 deletions(-)

diff --git a/scripts/scil_tractogram_point_math.py b/scripts/scil_tractogram_point_math.py
index e6224fc1e..d058bb4ea 100755
--- a/scripts/scil_tractogram_point_math.py
+++ b/scripts/scil_tractogram_point_math.py
@@ -66,14 +66,12 @@ def _build_arg_parser():
     p.add_argument('in_tractogram', metavar='INPUT_FILE',
                    help='Input tractogram containing streamlines and '
                         'metadata.')
-    p.add_argument('--in_dpp_name',  nargs='+',
-                   required=True,
+    p.add_argument('--in_dpp_name',  nargs='+', required=True,
                    help='Name or list of names of the data_per_point for '
                         'operation to be performed on. If more than one dpp '
                         'is selected, the same operation will be applied '
                         'separately to each one.')
-    p.add_argument('--out_name', nargs='+',
-                   required=True,
+    p.add_argument('--out_name', nargs='+', required=True,
                    help='Name of the resulting data_per_point or '
                    'data_per_streamline to be saved in the output '
                    'tractogram. If more than one --in_dpp_name was used, '
@@ -90,6 +88,7 @@ def _build_arg_parser():
                    help='If set, will overwrite the data_per_point or '
                    'data_per_streamline in the output tractogram, otherwise '
                    'previous data will be preserved in the output tractogram.')
+
     add_reference_arg(p)
     add_verbose_arg(p)
     add_overwrite_arg(p)
@@ -116,22 +115,23 @@ def main():
         logging.info("Input tractogram contains no streamlines. Exiting.")
         return
 
-    if len(args.in_dpp_name[0]) != len(args.out_name[0]):
+    if len(args.in_dpp_name) != len(args.out_name):
         parser.error('The number of in_dpp_names and out_names must be '
                      'the same.')
 
     # Check to see if there are duplicates in the out_names
-    if len(args.out_name[0]) != len(set(args.out_name[0])):
+    if len(args.out_name) != len(set(args.out_name)):
         parser.error('The output names (out_names) must be unique.')
 
     # Input name checks
-    for in_dpp_name in args.in_dpp_name[0]:
+    for in_dpp_name in args.in_dpp_name:
         # Check to see if the data per point exists.
         if in_dpp_name not in sft.data_per_point:
             logging.info('Data per point {} not found in input tractogram.'
                          .format(in_dpp_name))
             return
 
+        # Check if first data_per_point is multivalued
         data_shape = sft.data_per_point[in_dpp_name][0].shape
         if args.operation == 'correlation' and len(data_shape) == 1:
             logging.info('Correlation operation requires multivalued data per '
@@ -142,17 +142,17 @@ def main():
             logging.info('Correlation operation requires dps mode. Exiting.')
             return
 
-        if args.overwrite_data:
-            if in_dpp_name in args.out_name[0]:
+        if not args.overwrite_data:
+            if in_dpp_name in args.out_name:
                 logging.info('out_name {} already exists in input tractogram. '
-                             'Unset overwrite_data or choose a different '
+                             'Set overwrite_data or choose a different '
                              'out_name. Exiting.'.format(in_dpp_name))
                 return
 
     data_per_point = {}
     data_per_streamline = {}
-    for in_dpp_name, out_name in zip(args.in_dpp_name[0],
-                                     args.out_name[0]):
+    for in_dpp_name, out_name in zip(args.in_dpp_name,
+                                     args.out_name):
 
 
         # Perform the requested operation.
diff --git a/scripts/scil_tractogram_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
index a7a76ac20..c90cc9456 100755
--- a/scripts/scil_tractogram_project_map_to_streamlines.py
+++ b/scripts/scil_tractogram_project_map_to_streamlines.py
@@ -5,7 +5,7 @@
 Projects metrics extracted from a map onto the endpoints of streamlines.
 
 The default options will take data from a nifti image (3D or ND) and
-project it onto the endpoints of streamlines.
+project it onto the points of streamlines.
 """
 
 import argparse
@@ -35,7 +35,7 @@ def _build_arg_parser():
                    help='Fiber bundle file.')
     p.add_argument('out_tractogram',
                    help='Output file.')
-    p.add_argument('--in_metric', nargs='+', required=True,
+    p.add_argument('--in_maps', nargs='+', required=True,
                    help='Nifti metric to project onto streamlines.')
     p.add_argument('--out_dpp_name', nargs='+', required=True,
                    help='Name of the data_per_point to be saved in the \n'
@@ -46,12 +46,15 @@ def _build_arg_parser():
                    help='If set, will use trilinear interpolation \n'
                         'else will use nearest neighbor interpolation \n'
                         'by default.')
-
     p.add_argument('--endpoints_only', action='store_true',
                    help='If set, will only project the metric onto the \n'
                    'endpoints of the streamlines (all other values along \n'
                    ' streamlines will be NaN). If not set, will project \n'
                    ' the metric onto all points of the streamlines.')
+    p.add_argument('--overwrite_data', action='store_true', default=False,
+                   help='If set, will overwrite data_per_point in the '
+                   'output tractogram, otherwise previous data will be '
+                   'preserved in the output tractogram.')
 
     add_reference_arg(p)
     add_overwrite_arg(p)
@@ -63,10 +66,7 @@ def main():
     parser = _build_arg_parser()
     args = parser.parse_args()
 
-    input_file_list = [args.in_tractogram]
-    for fmetric in args.in_metric:
-        input_file_list += fmetric
-    assert_inputs_exist(parser, input_file_list)
+    assert_inputs_exist(parser, [args.in_tractogram] + args.in_maps)
 
     assert_outputs_exist(parser, args, [args.out_tractogram])
 
@@ -76,15 +76,28 @@ def main():
     sft.to_corner()
 
     if len(sft.streamlines) == 0:
-        logging.warning('Empty bundle file {}. Skipping'.format(args.bundle))
+        logging.warning('Empty bundle file {}. Skipping'.format(args.in_tractogram))
         return
 
     # Check to see if the number of metrics and dpp_names are the same
-    if len(args.in_metric) != len(args.out_dpp_name):
+    if len(args.in_maps) != len(args.out_dpp_name):
         parser.error('The number of metrics and dpp_names must be the same.')
 
+    # Check to see if there are duplicates in the out_dpp_names
+    if len(args.out_dpp_name) != len(set(args.out_dpp_name)):
+        parser.error('The output names (out_dpp_names) must be unique.')
+
+    # Check to see if the output names already exist in the input tractogram
+    if not args.overwrite_data:
+        for out_dpp_name in args.out_dpp_name:
+            if out_dpp_name in sft.data_per_point:
+                logging.info('out_name {} already exists in input tractogram. '
+                             'Set overwrite_data or choose a different '
+                             'out_name. Exiting.'.format(out_dpp_name))
+                return
+
     data_per_point = {}
-    for fmetric, dpp_name in zip(args.in_metric[0], args.out_dpp_name[0]):
+    for fmetric, dpp_name in zip(args.in_maps, args.out_dpp_name):
         logging.debug("Loading the metric...")
         metric_img, metric_dtype = load_img(fmetric)
         metric_data = metric_img.get_fdata(caching='unchanged', dtype=float)
@@ -106,9 +119,17 @@ def main():
 
         data_per_point[dpp_name] = streamline_data
 
-    out_sft = StatefulTractogram(sft.streamlines, metric_img,
-                                 sft.space, sft.origin,
-                                 data_per_point=data_per_point)
+    if args.overwrite_data:
+        out_sft = sft.from_sft(sft.streamlines, sft,
+                               data_per_point=data_per_point)
+    else:
+        old_data_per_point = sft.data_per_point
+        for dpp_name in data_per_point:
+            old_data_per_point[dpp_name] = data_per_point[dpp_name]
+        out_sft = sft.from_sft(sft.streamlines, sft,
+                               data_per_point=old_data_per_point)
+
+    print(out_sft.data_per_point)
     save_tractogram(out_sft, args.out_tractogram)
 
 

From e679fa13272d484ae3dc1551620372e7102d4ec9 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Tue, 30 Jan 2024 14:48:12 -0500
Subject: [PATCH 41/97] fixed project map tests

---
 .../test_tractogram_project_map_to_streamlines.py      | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/scripts/tests/test_tractogram_project_map_to_streamlines.py b/scripts/tests/test_tractogram_project_map_to_streamlines.py
index c4b171490..ce3b125fe 100644
--- a/scripts/tests/test_tractogram_project_map_to_streamlines.py
+++ b/scripts/tests/test_tractogram_project_map_to_streamlines.py
@@ -25,7 +25,7 @@ def test_execution_3D_map(script_runner):
 
     ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
                             in_tracto_1, 't1_on_streamlines.trk',
-                            '--in_metric', in_t1,
+                            '--in_maps', in_t1,
                             '--out_dpp_name', 't1')
     assert ret.success
 
@@ -38,7 +38,7 @@ def test_execution_4D_map(script_runner):
 
     ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
                             in_tracto_1, 'rgb_on_streamlines.trk',
-                            '--in_metric', in_rgb,
+                            '--in_maps', in_rgb,
                             '--out_dpp_name', 'rgb')
     assert ret.success
 
@@ -52,7 +52,7 @@ def test_execution_3D_map_endpoints_only(script_runner):
     ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
                             in_tracto_1,
                             't1_on_streamlines_endpoints.trk',
-                            '--in_metric', in_t1,
+                            '--in_maps', in_t1,
                             '--out_dpp_name', 't1',
                             '--endpoints_only')
     assert ret.success
@@ -67,7 +67,7 @@ def test_execution_4D_map_endpoints_only(script_runner):
     ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
                             in_tracto_1,
                             'rgb_on_streamlines_endpoints.trk',
-                            '--in_metric', in_rgb,
+                            '--in_maps', in_rgb,
                             '--out_dpp_name', 'rgb',
                             '--endpoints_only')
     assert ret.success
@@ -82,7 +82,7 @@ def test_execution_3D_map_trilinear(script_runner):
     ret = script_runner.run('scil_tractogram_project_map_to_streamlines.py',
                             in_tracto_1,
                             't1_on_streamlines_trilinear.trk',
-                            '--in_metric', in_t1,
+                            '--in_maps', in_t1,
                             '--out_dpp_name', 't1',
                             '--trilinear')
     assert ret.success

From 4046cc11b5f7fcb5cd80fc5f8649aa46450258ae Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Tue, 30 Jan 2024 14:49:50 -0500
Subject: [PATCH 42/97] rm doc reference to endpoints

---
 scripts/scil_tractogram_project_map_to_streamlines.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/scil_tractogram_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
index c90cc9456..f702dd2d0 100755
--- a/scripts/scil_tractogram_project_map_to_streamlines.py
+++ b/scripts/scil_tractogram_project_map_to_streamlines.py
@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 
 """
-Projects metrics extracted from a map onto the endpoints of streamlines.
+Projects metrics extracted from a map onto the points of streamlines.
 
 The default options will take data from a nifti image (3D or ND) and
 project it onto the points of streamlines.

From 0c5cdd3fa2319c7d906918ba61de72c33992e12a Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Tue, 30 Jan 2024 14:53:16 -0500
Subject: [PATCH 43/97] update test tractogram point math new args

---
 scripts/tests/test_tractogram_point_math.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/scripts/tests/test_tractogram_point_math.py b/scripts/tests/test_tractogram_point_math.py
index 99ab6c966..f819f2523 100644
--- a/scripts/tests/test_tractogram_point_math.py
+++ b/scripts/tests/test_tractogram_point_math.py
@@ -29,11 +29,12 @@ def test_execution_tractogram_point_math_mean_3D_defaults(script_runner):
 
     script_runner.run('scil_tractogram_project_map_to_streamlines.py',
                       in_bundle, t1_on_bundle,
-                      '--in_metric', in_t1,
+                      '--in_maps', in_t1,
                       '--out_dpp_name', 't1')
 
     ret = script_runner.run('scil_tractogram_point_math.py',
                             'mean',
+                            'dps',
                             t1_on_bundle,
                             't1_mean_on_streamlines.trk',
                             '--in_dpp_name', 't1',
@@ -53,11 +54,12 @@ def test_execution_tractogram_point_math_mean_4D_correlation(script_runner):
 
     script_runner.run('scil_tractogram_project_map_to_streamlines.py',
                       in_bundle, fodf_on_bundle,
-                      '--in_metric', in_fodf, in_fodf,
+                      '--in_maps', in_fodf, in_fodf,
                       '--out_dpp_name', 'fodf', 'fodf2')
 
     ret = script_runner.run('scil_tractogram_point_math.py',
                             'correlation',
+                            'dps',
                             fodf_on_bundle,
                             'fodf_correlation_on_streamlines.trk',
                             '--in_dpp_name', 'fodf',

From 0963198c2f3eb2cc5adc60a4adc4d58681536bb6 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Tue, 30 Jan 2024 14:57:33 -0500
Subject: [PATCH 44/97] updated name of to dpp_math

---
 ...tractogram_point_math.py => scil_tractogram_dpp_math.py} | 0
 ...tractogram_point_math.py => test_tractogram_dpp_math.py} | 6 +++---
 2 files changed, 3 insertions(+), 3 deletions(-)
 rename scripts/{scil_tractogram_point_math.py => scil_tractogram_dpp_math.py} (100%)
 rename scripts/tests/{test_tractogram_point_math.py => test_tractogram_dpp_math.py} (92%)

diff --git a/scripts/scil_tractogram_point_math.py b/scripts/scil_tractogram_dpp_math.py
similarity index 100%
rename from scripts/scil_tractogram_point_math.py
rename to scripts/scil_tractogram_dpp_math.py
diff --git a/scripts/tests/test_tractogram_point_math.py b/scripts/tests/test_tractogram_dpp_math.py
similarity index 92%
rename from scripts/tests/test_tractogram_point_math.py
rename to scripts/tests/test_tractogram_dpp_math.py
index f819f2523..ef89d6eca 100644
--- a/scripts/tests/test_tractogram_point_math.py
+++ b/scripts/tests/test_tractogram_dpp_math.py
@@ -14,7 +14,7 @@
 
 
 def test_help_option(script_runner):
-    ret = script_runner.run('scil_tractogram_point_math.py', '--help')
+    ret = script_runner.run('scil_tractogram_dpp_math.py', '--help')
     assert ret.success
 
 
@@ -32,7 +32,7 @@ def test_execution_tractogram_point_math_mean_3D_defaults(script_runner):
                       '--in_maps', in_t1,
                       '--out_dpp_name', 't1')
 
-    ret = script_runner.run('scil_tractogram_point_math.py',
+    ret = script_runner.run('scil_tractogram_dpp_math.py',
                             'mean',
                             'dps',
                             t1_on_bundle,
@@ -57,7 +57,7 @@ def test_execution_tractogram_point_math_mean_4D_correlation(script_runner):
                       '--in_maps', in_fodf, in_fodf,
                       '--out_dpp_name', 'fodf', 'fodf2')
 
-    ret = script_runner.run('scil_tractogram_point_math.py',
+    ret = script_runner.run('scil_tractogram_dpp_math.py',
                             'correlation',
                             'dps',
                             fodf_on_bundle,

From ff8c3779e3614d378eacf4e4043ed452518e2c8c Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Tue, 30 Jan 2024 15:12:42 -0500
Subject: [PATCH 45/97] update doc for clearer on what happens in 4D case

---
 scripts/scil_tractogram_project_map_to_streamlines.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/scripts/scil_tractogram_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
index f702dd2d0..1be51496d 100755
--- a/scripts/scil_tractogram_project_map_to_streamlines.py
+++ b/scripts/scil_tractogram_project_map_to_streamlines.py
@@ -4,8 +4,10 @@
 """
 Projects metrics extracted from a map onto the points of streamlines.
 
-The default options will take data from a nifti image (3D or ND) and
-project it onto the points of streamlines.
+The default options will take data from a nifti image (3D or 4D) and
+project it onto the points of streamlines. If the image is 4D, the data
+is stored as a list of 1D arrays per streamline. If the image is 3D, the data is stored
+as a list of values per streamline.
 """
 
 import argparse

From d3fd65ac0c6361fda0697f64cbc4d418e598251b Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Tue, 30 Jan 2024 15:44:28 -0500
Subject: [PATCH 46/97] remove print

---
 scripts/scil_tractogram_project_map_to_streamlines.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/scripts/scil_tractogram_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
index 1be51496d..eb37f2c02 100755
--- a/scripts/scil_tractogram_project_map_to_streamlines.py
+++ b/scripts/scil_tractogram_project_map_to_streamlines.py
@@ -131,7 +131,6 @@ def main():
         out_sft = sft.from_sft(sft.streamlines, sft,
                                data_per_point=old_data_per_point)
 
-    print(out_sft.data_per_point)
     save_tractogram(out_sft, args.out_tractogram)
 
 

From 0778e9613a899addfcf1101b2f3bed1566f512c5 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 5 Feb 2024 11:00:55 -0500
Subject: [PATCH 47/97] moved project func to new file

---
 scilpy/tractograms/dps_and_dpp_management.py  | 65 +++++++++++++++++++
 scilpy/tractograms/streamline_operations.py   | 65 -------------------
 ...l_tractogram_project_map_to_streamlines.py |  2 +-
 3 files changed, 66 insertions(+), 66 deletions(-)
 create mode 100644 scilpy/tractograms/dps_and_dpp_management.py

diff --git a/scilpy/tractograms/dps_and_dpp_management.py b/scilpy/tractograms/dps_and_dpp_management.py
new file mode 100644
index 000000000..a365b1a79
--- /dev/null
+++ b/scilpy/tractograms/dps_and_dpp_management.py
@@ -0,0 +1,65 @@
+import numpy as np
+
+def project_metric_to_streamlines(sft, metric, endpoints_only=False):
+    """
+    Projects a metric onto the points of streamlines.
+
+    Parameters
+    ----------
+    sft: StatefulTractogram
+        Input tractogram.
+    metric: DataVolume
+        Input metric.
+
+    Optional:
+    ---------
+    endpoints_only: bool
+        If True, will only project the metric onto the endpoints of the
+        streamlines (all values along streamlines set to zero). If False,
+        will project the metric onto all points of the streamlines.
+
+    Returns
+    -------
+    streamline_data:
+        metric projected to each point of the streamlines.
+    """
+    if len(metric.data.shape) == 4:
+        dimension = metric.data.shape[3]
+    else:
+        dimension = 1
+
+    streamline_data = []
+    if endpoints_only:
+        for s in sft.streamlines:
+            p1_data = metric.get_value_at_coordinate(
+                s[0][0], s[0][1], s[0][2],
+                space=sft.space, origin=sft.origin)
+            p2_data = metric.get_value_at_coordinate(
+                s[-1][0], s[-1][1], s[-1][2],
+                space=sft.space, origin=sft.origin)
+            thisstreamline_data = []
+            if dimension == 1:
+                thisstreamline_data = np.ones((len(s), 1)) * np.nan
+            else:
+                thisstreamline_data = np.ones(
+                    (len(s), p1_data.shape[0])) * np.nan
+
+            thisstreamline_data[0] = p1_data
+            thisstreamline_data[-1] = p2_data
+            thisstreamline_data = np.asarray(thisstreamline_data)
+
+            streamline_data.append(
+                np.reshape(thisstreamline_data,
+                           (len(thisstreamline_data), dimension)))
+    else:
+        for s in sft.streamlines:
+            thisstreamline_data = []
+            for p in s:
+                thisstreamline_data.append(metric.get_value_at_coordinate(
+                    p[0], p[1], p[2], space=sft.space, origin=sft.origin))
+
+            streamline_data.append(
+                np.reshape(thisstreamline_data,
+                           (len(thisstreamline_data), dimension)))
+
+    return streamline_data
diff --git a/scilpy/tractograms/streamline_operations.py b/scilpy/tractograms/streamline_operations.py
index 8e053fe08..2d0bdf2c7 100644
--- a/scilpy/tractograms/streamline_operations.py
+++ b/scilpy/tractograms/streamline_operations.py
@@ -527,68 +527,3 @@ def stream_correlation(array1, array2):
     'max': stream_max,
     'correlation': stream_correlation,
 }
-
-
-def project_metric_to_streamlines(sft, metric, endpoints_only=False):
-    """
-    Projects a metric onto the points of streamlines.
-
-    Parameters
-    ----------
-    sft: StatefulTractogram
-        Input tractogram.
-    metric: DataVolume
-        Input metric.
-
-    Optional:
-    ---------
-    endpoints_only: bool
-        If True, will only project the metric onto the endpoints of the
-        streamlines (all values along streamlines set to zero). If False,
-        will project the metric onto all points of the streamlines.
-
-    Returns
-    -------
-    streamline_data:
-        metric projected to each point of the streamlines.
-    """
-    if len(metric.data.shape) == 4:
-        dimension = metric.data.shape[3]
-    else:
-        dimension = 1
-
-    streamline_data = []
-    if endpoints_only:
-        for s in sft.streamlines:
-            p1_data = metric.get_value_at_coordinate(
-                s[0][0], s[0][1], s[0][2],
-                space=sft.space, origin=sft.origin)
-            p2_data = metric.get_value_at_coordinate(
-                s[-1][0], s[-1][1], s[-1][2],
-                space=sft.space, origin=sft.origin)
-            thisstreamline_data = []
-            if dimension == 1:
-                thisstreamline_data = np.ones((len(s), 1)) * np.nan
-            else:
-                thisstreamline_data = np.ones(
-                    (len(s), p1_data.shape[0])) * np.nan
-
-            thisstreamline_data[0] = p1_data
-            thisstreamline_data[-1] = p2_data
-            thisstreamline_data = np.asarray(thisstreamline_data)
-
-            streamline_data.append(
-                np.reshape(thisstreamline_data,
-                           (len(thisstreamline_data), dimension)))
-    else:
-        for s in sft.streamlines:
-            thisstreamline_data = []
-            for p in s:
-                thisstreamline_data.append(metric.get_value_at_coordinate(
-                    p[0], p[1], p[2], space=sft.space, origin=sft.origin))
-
-            streamline_data.append(
-                np.reshape(thisstreamline_data,
-                           (len(thisstreamline_data), dimension)))
-
-    return streamline_data
diff --git a/scripts/scil_tractogram_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
index eb37f2c02..c6578bbc9 100755
--- a/scripts/scil_tractogram_project_map_to_streamlines.py
+++ b/scripts/scil_tractogram_project_map_to_streamlines.py
@@ -23,7 +23,7 @@
                              assert_inputs_exist,
                              assert_outputs_exist)
 from scilpy.image.volume_space_management import DataVolume
-from scilpy.tractograms.streamline_operations import (
+from scilpy.tractograms.dps_and_dpp_management import (
     project_metric_to_streamlines)
 
 

From 918d4c279f74937cecdc7fd8359aa63f46c3cfc1 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 5 Feb 2024 11:03:00 -0500
Subject: [PATCH 48/97] changed metric to map

---
 scilpy/tractograms/dps_and_dpp_management.py | 24 ++++++++++----------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/scilpy/tractograms/dps_and_dpp_management.py b/scilpy/tractograms/dps_and_dpp_management.py
index a365b1a79..cf79189be 100644
--- a/scilpy/tractograms/dps_and_dpp_management.py
+++ b/scilpy/tractograms/dps_and_dpp_management.py
@@ -1,40 +1,40 @@
 import numpy as np
 
-def project_metric_to_streamlines(sft, metric, endpoints_only=False):
+def project_map_to_streamlines(sft, map, endpoints_only=False):
     """
-    Projects a metric onto the points of streamlines.
+    Projects a map onto the points of streamlines.
 
     Parameters
     ----------
     sft: StatefulTractogram
         Input tractogram.
-    metric: DataVolume
-        Input metric.
+    map: DataVolume
+        Input map.
 
     Optional:
     ---------
     endpoints_only: bool
-        If True, will only project the metric onto the endpoints of the
+        If True, will only project the map onto the endpoints of the
         streamlines (all values along streamlines set to zero). If False,
-        will project the metric onto all points of the streamlines.
+        will project the map onto all points of the streamlines.
 
     Returns
     -------
     streamline_data:
-        metric projected to each point of the streamlines.
+        map projected to each point of the streamlines.
     """
-    if len(metric.data.shape) == 4:
-        dimension = metric.data.shape[3]
+    if len(map.data.shape) == 4:
+        dimension = map.data.shape[3]
     else:
         dimension = 1
 
     streamline_data = []
     if endpoints_only:
         for s in sft.streamlines:
-            p1_data = metric.get_value_at_coordinate(
+            p1_data = map.get_value_at_coordinate(
                 s[0][0], s[0][1], s[0][2],
                 space=sft.space, origin=sft.origin)
-            p2_data = metric.get_value_at_coordinate(
+            p2_data = map.get_value_at_coordinate(
                 s[-1][0], s[-1][1], s[-1][2],
                 space=sft.space, origin=sft.origin)
             thisstreamline_data = []
@@ -55,7 +55,7 @@ def project_metric_to_streamlines(sft, metric, endpoints_only=False):
         for s in sft.streamlines:
             thisstreamline_data = []
             for p in s:
-                thisstreamline_data.append(metric.get_value_at_coordinate(
+                thisstreamline_data.append(map.get_value_at_coordinate(
                     p[0], p[1], p[2], space=sft.space, origin=sft.origin))
 
             streamline_data.append(

From ce94ab07dd428c2f60ad158c8a3a32680d1fdaf6 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 5 Feb 2024 11:04:18 -0500
Subject: [PATCH 49/97] changed metric to map

---
 ...l_tractogram_project_map_to_streamlines.py | 32 +++++++++----------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/scripts/scil_tractogram_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
index c6578bbc9..d31e31d35 100755
--- a/scripts/scil_tractogram_project_map_to_streamlines.py
+++ b/scripts/scil_tractogram_project_map_to_streamlines.py
@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 
 """
-Projects metrics extracted from a map onto the points of streamlines.
+Projects maps extracted from a map onto the points of streamlines.
 
 The default options will take data from a nifti image (3D or 4D) and
 project it onto the points of streamlines. If the image is 4D, the data
@@ -24,7 +24,7 @@
                              assert_outputs_exist)
 from scilpy.image.volume_space_management import DataVolume
 from scilpy.tractograms.dps_and_dpp_management import (
-    project_metric_to_streamlines)
+    project_map_to_streamlines)
 
 
 def _build_arg_parser():
@@ -38,7 +38,7 @@ def _build_arg_parser():
     p.add_argument('out_tractogram',
                    help='Output file.')
     p.add_argument('--in_maps', nargs='+', required=True,
-                   help='Nifti metric to project onto streamlines.')
+                   help='Nifti map to project onto streamlines.')
     p.add_argument('--out_dpp_name', nargs='+', required=True,
                    help='Name of the data_per_point to be saved in the \n'
                    'output tractogram.')
@@ -49,10 +49,10 @@ def _build_arg_parser():
                         'else will use nearest neighbor interpolation \n'
                         'by default.')
     p.add_argument('--endpoints_only', action='store_true',
-                   help='If set, will only project the metric onto the \n'
+                   help='If set, will only project the map onto the \n'
                    'endpoints of the streamlines (all other values along \n'
                    ' streamlines will be NaN). If not set, will project \n'
-                   ' the metric onto all points of the streamlines.')
+                   ' the map onto all points of the streamlines.')
     p.add_argument('--overwrite_data', action='store_true', default=False,
                    help='If set, will overwrite data_per_point in the '
                    'output tractogram, otherwise previous data will be '
@@ -81,9 +81,9 @@ def main():
         logging.warning('Empty bundle file {}. Skipping'.format(args.in_tractogram))
         return
 
-    # Check to see if the number of metrics and dpp_names are the same
+    # Check to see if the number of maps and dpp_names are the same
     if len(args.in_maps) != len(args.out_dpp_name):
-        parser.error('The number of metrics and dpp_names must be the same.')
+        parser.error('The number of maps and dpp_names must be the same.')
 
     # Check to see if there are duplicates in the out_dpp_names
     if len(args.out_dpp_name) != len(set(args.out_dpp_name)):
@@ -99,22 +99,22 @@ def main():
                 return
 
     data_per_point = {}
-    for fmetric, dpp_name in zip(args.in_maps, args.out_dpp_name):
-        logging.debug("Loading the metric...")
-        metric_img, metric_dtype = load_img(fmetric)
-        metric_data = metric_img.get_fdata(caching='unchanged', dtype=float)
-        metric_res = metric_img.header.get_zooms()[:3]
+    for fmap, dpp_name in zip(args.in_maps, args.out_dpp_name):
+        logging.debug("Loading the map...")
+        map_img, map_dtype = load_img(fmap)
+        map_data = map_img.get_fdata(caching='unchanged', dtype=float)
+        map_res = map_img.header.get_zooms()[:3]
 
         if args.trilinear:
             interp = "trilinear"
         else:
             interp = "nearest"
 
-        metric = DataVolume(metric_data, metric_res, interp)
+        map = DataVolume(map_data, map_res, interp)
 
-        logging.debug("Projecting metric onto streamlines")
-        streamline_data = project_metric_to_streamlines(
-            sft, metric,
+        logging.debug("Projecting map onto streamlines")
+        streamline_data = project_map_to_streamlines(
+            sft, map,
             endpoints_only=args.endpoints_only)
 
         logging.debug("Saving the tractogram...")

From 75a54bff072bd88551ad345fd7de4cdb714f807a Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 5 Feb 2024 11:08:11 -0500
Subject: [PATCH 50/97] added dummy test for dpp management

---
 scilpy/tractograms/tests/test_dps_and_dpp_management.py | 3 +++
 scilpy/tractograms/tests/test_streamline_operations.py  | 5 -----
 2 files changed, 3 insertions(+), 5 deletions(-)
 create mode 100644 scilpy/tractograms/tests/test_dps_and_dpp_management.py

diff --git a/scilpy/tractograms/tests/test_dps_and_dpp_management.py b/scilpy/tractograms/tests/test_dps_and_dpp_management.py
new file mode 100644
index 000000000..fb93d736a
--- /dev/null
+++ b/scilpy/tractograms/tests/test_dps_and_dpp_management.py
@@ -0,0 +1,3 @@
+def test_project_map_to_streamlines():
+    # toDo
+    pass
diff --git a/scilpy/tractograms/tests/test_streamline_operations.py b/scilpy/tractograms/tests/test_streamline_operations.py
index b37c4aec7..f8e0d4e8a 100644
--- a/scilpy/tractograms/tests/test_streamline_operations.py
+++ b/scilpy/tractograms/tests/test_streamline_operations.py
@@ -369,11 +369,6 @@ def test_smooth_line_spline():
     assert dist_1 < dist_2
 
 
-def test_project_metric_to_streamlines():
-    # toDo
-    pass
-
-
 def test_perform_streamline_operation_per_point():
     # toDo
     pass

From 74d6a8714487119f545aa11631944fda71c87e98 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 5 Feb 2024 11:59:43 -0500
Subject: [PATCH 51/97] 4D dps math - now outputs array per streamline

---
 scilpy/tractograms/streamline_operations.py        | 14 +++++++-------
 .../scil_tractogram_project_map_to_streamlines.py  |  2 +-
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/scilpy/tractograms/streamline_operations.py b/scilpy/tractograms/streamline_operations.py
index 2d0bdf2c7..8324d0e94 100644
--- a/scilpy/tractograms/streamline_operations.py
+++ b/scilpy/tractograms/streamline_operations.py
@@ -463,12 +463,13 @@ def perform_operation_per_streamline(op_name, sft, dpp_name='metric',
         for s in sft.data_per_point[dpp_name]:
             start = s[0]
             end = s[-1]
-            concat = np.concatenate((start[:], end[:]), axis=0)
+            concat = np.concatenate((start[:], end[:]))
             new_data_per_streamline.append(call_op(concat))
     else:
         new_data_per_streamline = []
         for s in sft.data_per_point[dpp_name]:
-            new_data_per_streamline.append(call_op(s[:]))
+            s_np = np.asarray(s)
+            new_data_per_streamline.append(call_op(s_np))
 
     return new_data_per_streamline
 
@@ -501,19 +502,18 @@ def perform_pairwise_streamline_operation_on_endpoints(op_name, sft, dpp_name='m
 
 
 def stream_mean(array):
-    return np.mean(array)
+    return np.squeeze(np.mean(array,axis=0))
 
 
 def stream_sum(array):
-    return np.sum(array)
+    return np.squeeze(np.sum(array,axis=0))
 
 
 def stream_min(array):
-    return np.min(array)
-
+    return np.squeeze(np.min(array,axis=0))
 
 def stream_max(array):
-    return np.max(array)
+    return np.squeeze(np.max(array,axis=0))
 
 
 def stream_correlation(array1, array2):
diff --git a/scripts/scil_tractogram_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
index d31e31d35..10e047f20 100755
--- a/scripts/scil_tractogram_project_map_to_streamlines.py
+++ b/scripts/scil_tractogram_project_map_to_streamlines.py
@@ -130,7 +130,7 @@ def main():
             old_data_per_point[dpp_name] = data_per_point[dpp_name]
         out_sft = sft.from_sft(sft.streamlines, sft,
                                data_per_point=old_data_per_point)
-
+    
     save_tractogram(out_sft, args.out_tractogram)
 
 

From 507df9ff9977247216803c4550d6d893625e397a Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 5 Feb 2024 12:15:25 -0500
Subject: [PATCH 52/97] pep8 issues

---
 scilpy/tractograms/dps_and_dpp_management.py          | 1 +
 scilpy/tractograms/streamline_operations.py           | 3 ++-
 scripts/scil_tractogram_dpp_math.py                   | 6 ++----
 scripts/scil_tractogram_project_map_to_streamlines.py | 9 +++++----
 4 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/scilpy/tractograms/dps_and_dpp_management.py b/scilpy/tractograms/dps_and_dpp_management.py
index cf79189be..373add8a5 100644
--- a/scilpy/tractograms/dps_and_dpp_management.py
+++ b/scilpy/tractograms/dps_and_dpp_management.py
@@ -1,5 +1,6 @@
 import numpy as np
 
+
 def project_map_to_streamlines(sft, map, endpoints_only=False):
     """
     Projects a map onto the points of streamlines.
diff --git a/scilpy/tractograms/streamline_operations.py b/scilpy/tractograms/streamline_operations.py
index 8324d0e94..1b5655cac 100644
--- a/scilpy/tractograms/streamline_operations.py
+++ b/scilpy/tractograms/streamline_operations.py
@@ -474,7 +474,8 @@ def perform_operation_per_streamline(op_name, sft, dpp_name='metric',
     return new_data_per_streamline
 
 
-def perform_pairwise_streamline_operation_on_endpoints(op_name, sft, dpp_name='metric'):
+def perform_pairwise_streamline_operation_on_endpoints(op_name, sft,
+                                                       dpp_name='metric'):
     """Peforms an operation across endpoints for each streamline.
 
     Parameters
diff --git a/scripts/scil_tractogram_dpp_math.py b/scripts/scil_tractogram_dpp_math.py
index d058bb4ea..92584a04d 100755
--- a/scripts/scil_tractogram_dpp_math.py
+++ b/scripts/scil_tractogram_dpp_math.py
@@ -153,13 +153,11 @@ def main():
     data_per_streamline = {}
     for in_dpp_name, out_name in zip(args.in_dpp_name,
                                      args.out_name):
-
-
         # Perform the requested operation.
         if args.operation == 'correlation':
             logging.info('Performing {} across endpoint data and saving as '
                          'new dpp {}'.format(
-                args.operation, out_name))
+                         args.operation, out_name))
             new_dps = perform_pairwise_streamline_operation_on_endpoints(
                 args.operation, sft, in_dpp_name)
 
@@ -182,7 +180,6 @@ def main():
                 args.operation, sft, in_dpp_name, args.endpoints_only)
             data_per_streamline[out_name] = new_data_per_streamline
 
-
     if args.overwrite_data:
         new_sft = sft.from_sft(sft.streamlines, sft,
                                data_per_point=data_per_point,
@@ -219,5 +216,6 @@ def main():
     save_tractogram(new_sft, args.out_tractogram,
                     bbox_valid_check=args.bbox_check)
 
+
 if __name__ == "__main__":
     main()
diff --git a/scripts/scil_tractogram_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
index 10e047f20..18d0a64ed 100755
--- a/scripts/scil_tractogram_project_map_to_streamlines.py
+++ b/scripts/scil_tractogram_project_map_to_streamlines.py
@@ -6,8 +6,8 @@
 
 The default options will take data from a nifti image (3D or 4D) and
 project it onto the points of streamlines. If the image is 4D, the data
-is stored as a list of 1D arrays per streamline. If the image is 3D, the data is stored
-as a list of values per streamline.
+is stored as a list of 1D arrays per streamline. If the image is 3D,
+the data is stored as a list of values per streamline.
 """
 
 import argparse
@@ -78,7 +78,8 @@ def main():
     sft.to_corner()
 
     if len(sft.streamlines) == 0:
-        logging.warning('Empty bundle file {}. Skipping'.format(args.in_tractogram))
+        logging.warning('Empty bundle file {}. Skipping'.format(
+            args.in_tractogram))
         return
 
     # Check to see if the number of maps and dpp_names are the same
@@ -130,7 +131,7 @@ def main():
             old_data_per_point[dpp_name] = data_per_point[dpp_name]
         out_sft = sft.from_sft(sft.streamlines, sft,
                                data_per_point=old_data_per_point)
-    
+
     save_tractogram(out_sft, args.out_tractogram)
 
 

From 3a59f6a2f7662497f689a14808ffd41dc65e1326 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Wed, 7 Feb 2024 14:14:07 -0500
Subject: [PATCH 53/97] pep8

---
 scilpy/tractograms/streamline_operations.py | 9 +++++----
 scripts/scil_tractogram_dpp_math.py         | 3 +--
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/scilpy/tractograms/streamline_operations.py b/scilpy/tractograms/streamline_operations.py
index 1b5655cac..3a98316e0 100644
--- a/scilpy/tractograms/streamline_operations.py
+++ b/scilpy/tractograms/streamline_operations.py
@@ -503,18 +503,19 @@ def perform_pairwise_streamline_operation_on_endpoints(op_name, sft,
 
 
 def stream_mean(array):
-    return np.squeeze(np.mean(array,axis=0))
+    return np.squeeze(np.mean(array, axis=0))
 
 
 def stream_sum(array):
-    return np.squeeze(np.sum(array,axis=0))
+    return np.squeeze(np.sum(array, axis=0))
 
 
 def stream_min(array):
-    return np.squeeze(np.min(array,axis=0))
+    return np.squeeze(np.min(array, axis=0))
+
 
 def stream_max(array):
-    return np.squeeze(np.max(array,axis=0))
+    return np.squeeze(np.max(array, axis=0))
 
 
 def stream_correlation(array1, array2):
diff --git a/scripts/scil_tractogram_dpp_math.py b/scripts/scil_tractogram_dpp_math.py
index 92584a04d..12034bf8f 100755
--- a/scripts/scil_tractogram_dpp_math.py
+++ b/scripts/scil_tractogram_dpp_math.py
@@ -156,8 +156,7 @@ def main():
         # Perform the requested operation.
         if args.operation == 'correlation':
             logging.info('Performing {} across endpoint data and saving as '
-                         'new dpp {}'.format(
-                         args.operation, out_name))
+                         'new dpp {}'.format(args.operation, out_name))
             new_dps = perform_pairwise_streamline_operation_on_endpoints(
                 args.operation, sft, in_dpp_name)
 

From 1f69f940a152f95625e7950afbe3069e2763ff6f Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Wed, 7 Feb 2024 14:14:47 -0500
Subject: [PATCH 54/97] remove py version file

---
 .python-version | 1 -
 1 file changed, 1 deletion(-)
 delete mode 100644 .python-version

diff --git a/.python-version b/.python-version
deleted file mode 100644
index c8cfe3959..000000000
--- a/.python-version
+++ /dev/null
@@ -1 +0,0 @@
-3.10

From 47d4a21fe4509382c0ffe298e37f9d024ee840c1 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Wed, 7 Feb 2024 14:15:19 -0500
Subject: [PATCH 55/97] added utf header

---
 scilpy/tractograms/dps_and_dpp_management.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scilpy/tractograms/dps_and_dpp_management.py b/scilpy/tractograms/dps_and_dpp_management.py
index 373add8a5..d919e4788 100644
--- a/scilpy/tractograms/dps_and_dpp_management.py
+++ b/scilpy/tractograms/dps_and_dpp_management.py
@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import numpy as np
 
 

From 8e8bb69838430c9e05c0d893b6ff0f46e6540576 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <graham.little.phd@gmail.com>
Date: Thu, 8 Feb 2024 14:24:01 -0500
Subject: [PATCH 56/97] removed py version file

---
 scripts/tests/.python-version | 1 -
 1 file changed, 1 deletion(-)
 delete mode 100644 scripts/tests/.python-version

diff --git a/scripts/tests/.python-version b/scripts/tests/.python-version
deleted file mode 100644
index c8cfe3959..000000000
--- a/scripts/tests/.python-version
+++ /dev/null
@@ -1 +0,0 @@
-3.10

From 9ea5ec0bdaa099b161a0f6f4e910332e65e639c2 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <graham.little.phd@gmail.com>
Date: Thu, 8 Feb 2024 14:29:37 -0500
Subject: [PATCH 57/97] added back py ver file in root

---
 .python-version | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 .python-version

diff --git a/.python-version b/.python-version
new file mode 100644
index 000000000..7c7a975f4
--- /dev/null
+++ b/.python-version
@@ -0,0 +1 @@
+3.10
\ No newline at end of file

From 2e801b7045795f24a7c4936fa7e712522da4f398 Mon Sep 17 00:00:00 2001
From: karp2601 <karp2601@dinf-0051-20b.DInf.fsci.usherbrooke.ca>
Date: Tue, 13 Feb 2024 09:57:45 -0500
Subject: [PATCH 58/97] Adding msmt support

---
 scripts/scil_frf_set_diffusivities.py       | 22 ++++++++++++++++----
 scripts/tests/test_frf_set_diffusivities.py | 23 ++++++++++++++++++---
 2 files changed, 38 insertions(+), 7 deletions(-)

diff --git a/scripts/scil_frf_set_diffusivities.py b/scripts/scil_frf_set_diffusivities.py
index 6ae138701..dbec3dbec 100755
--- a/scripts/scil_frf_set_diffusivities.py
+++ b/scripts/scil_frf_set_diffusivities.py
@@ -6,7 +6,8 @@
 Use this script when you want to use a fixed response function
 and keep the mean b0.
 
-The FRF file is obtained from scil_frf_ssst.py
+The FRF file is obtained from scil_frf_ssst.py or scil_frf_msmt.py in the case
+of multi-shell data.
 
 Formerly: scil_set_response_function.py
 """
@@ -30,7 +31,9 @@ def _build_arg_parser():
     p.add_argument('new_frf', metavar='tuple',
                    help='Replace the response function with\n'
                         'this fiber response function x 10**-4 (e.g. '
-                        '15,4,4).')
+                        '15,4,4). \nIf multi-shell, write the first shell'
+                        ', then the second shell, \nand the third, etc '
+                        '(e.g. 15,4,4,13,5,5,12,5,5).')
     p.add_argument('output_frf_file', metavar='output',
                    help='Path of the new FRF file.')
     p.add_argument('--no_factor', action='store_true',
@@ -51,13 +54,24 @@ def main():
     assert_inputs_exist(parser, args.frf_file)
     assert_outputs_exist(parser, args, args.output_frf_file)
 
-    frf_file = np.array(np.loadtxt(args.frf_file))
+    frf_file = np.array(np.loadtxt(args.frf_file)).T
     new_frf = np.array(literal_eval(args.new_frf), dtype=np.float64)
     if not args.no_factor:
         new_frf *= 10 ** -4
     b0_mean = frf_file[3]
 
-    response = np.concatenate([new_frf, [b0_mean]])
+    if new_frf.shape[0] % 3 != 0:
+        raise ValueError('Inputed new frf is not valid. There should be '
+                         'three values per shell, and thus the total number '
+                         'of values should be a multiple of three.')
+
+    nb_shells = int(new_frf.shape[0] / 3)
+    new_frf = new_frf.reshape((nb_shells, 3))
+
+    response = np.empty((nb_shells, 4))
+    response[:, 0:3] = new_frf
+    response[:, 3] = b0_mean
+
     np.savetxt(args.output_frf_file, response)
 
 
diff --git a/scripts/tests/test_frf_set_diffusivities.py b/scripts/tests/test_frf_set_diffusivities.py
index 631796cde..9ceaeb0fa 100644
--- a/scripts/tests/test_frf_set_diffusivities.py
+++ b/scripts/tests/test_frf_set_diffusivities.py
@@ -7,7 +7,8 @@
 from scilpy.io.fetcher import fetch_data, get_home, get_testing_files_dict
 
 # If they already exist, this only takes 5 seconds (check md5sum)
-fetch_data(get_testing_files_dict(), keys=['processing.zip'])
+fetch_data(get_testing_files_dict(),
+           keys=['processing.zip', 'commit_amico.zip'])
 tmp_dir = tempfile.TemporaryDirectory()
 
 
@@ -16,10 +17,26 @@ def test_help_option(script_runner):
     assert ret.success
 
 
-def test_execution_processing(script_runner):
+def test_execution_processing_ssst(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_frf = os.path.join(get_home(), 'processing',
                           'frf.txt')
     ret = script_runner.run('scil_frf_set_diffusivities.py', in_frf,
-                            '15,4,4', 'nfrf.txt')
+                            '15,4,4', 'new_frf.txt', '-f')
     assert ret.success
+
+def test_execution_processing_msmt(script_runner):
+    os.chdir(os.path.expanduser(tmp_dir.name))
+    in_frf = os.path.join(get_home(), 'commit_amico',
+                          'wm_frf.txt')
+    ret = script_runner.run('scil_frf_set_diffusivities.py', in_frf,
+                            '15,4,4,13,4,4,12,5,5', 'new_frf.txt', '-f')
+    assert ret.success
+
+def test_execution_processing__wrong_input(script_runner):
+    os.chdir(os.path.expanduser(tmp_dir.name))
+    in_frf = os.path.join(get_home(), 'commit_amico',
+                          'wm_frf.txt')
+    ret = script_runner.run('scil_frf_set_diffusivities.py', in_frf,
+                            '15,4,4,13,4,4', 'new_frf.txt', '-f')
+    assert not ret.success

From 828b90d99aa44f09386b281f01843c8e62df8821 Mon Sep 17 00:00:00 2001
From: karp2601 <karp2601@dinf-0051-20b.DInf.fsci.usherbrooke.ca>
Date: Tue, 13 Feb 2024 10:01:42 -0500
Subject: [PATCH 59/97] Pep 8

---
 scripts/tests/test_frf_set_diffusivities.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/scripts/tests/test_frf_set_diffusivities.py b/scripts/tests/test_frf_set_diffusivities.py
index 9ceaeb0fa..673df6e74 100644
--- a/scripts/tests/test_frf_set_diffusivities.py
+++ b/scripts/tests/test_frf_set_diffusivities.py
@@ -25,6 +25,7 @@ def test_execution_processing_ssst(script_runner):
                             '15,4,4', 'new_frf.txt', '-f')
     assert ret.success
 
+
 def test_execution_processing_msmt(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_frf = os.path.join(get_home(), 'commit_amico',
@@ -33,6 +34,7 @@ def test_execution_processing_msmt(script_runner):
                             '15,4,4,13,4,4,12,5,5', 'new_frf.txt', '-f')
     assert ret.success
 
+
 def test_execution_processing__wrong_input(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_frf = os.path.join(get_home(), 'commit_amico',

From be217c7345cce2a1db2968accbc1cddfa738c2e2 Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Thu, 14 Dec 2023 11:58:32 -0500
Subject: [PATCH 60/97] normalize_bvecs: Remove unused variable (verified in
 all of our scripts)

---
 scilpy/gradients/bvec_bval_tools.py | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/scilpy/gradients/bvec_bval_tools.py b/scilpy/gradients/bvec_bval_tools.py
index 88c13f61e..8893fa1e1 100644
--- a/scilpy/gradients/bvec_bval_tools.py
+++ b/scilpy/gradients/bvec_bval_tools.py
@@ -37,7 +37,7 @@ def is_normalized_bvecs(bvecs):
                                 bvecs_norm == 0))
 
 
-def normalize_bvecs(bvecs, filename=None):
+def normalize_bvecs(bvecs):
     """
     Normalize b-vectors
 
@@ -45,8 +45,6 @@ def normalize_bvecs(bvecs, filename=None):
     ----------
     bvecs : (N, 3) array
         input b-vectors (N, 3) array
-    filename : string
-        output filename where to save the normalized bvecs
 
     Returns
     -------
@@ -58,10 +56,6 @@ def normalize_bvecs(bvecs, filename=None):
     idx = bvecs_norm != 0
     bvecs[idx] /= bvecs_norm[idx, None]
 
-    if filename is not None:
-        logging.info('Saving new bvecs: {}'.format(filename))
-        np.savetxt(filename, np.transpose(bvecs), "%.8f")
-
     return bvecs
 
 

From b2b93f81f65597c4c56a8545697a666733a314aa Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Thu, 14 Dec 2023 12:22:22 -0500
Subject: [PATCH 61/97] Prepare tests

---
 scilpy/gradients/tests/test_bvec_bval_tools.py | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/scilpy/gradients/tests/test_bvec_bval_tools.py b/scilpy/gradients/tests/test_bvec_bval_tools.py
index 92d005ee7..5f0db7498 100644
--- a/scilpy/gradients/tests/test_bvec_bval_tools.py
+++ b/scilpy/gradients/tests/test_bvec_bval_tools.py
@@ -1,17 +1,22 @@
 # -*- coding: utf-8 -*-
 import numpy as np
 
-from scilpy.gradients.bvec_bval_tools import round_bvals_to_shell
+from scilpy.gradients.bvec_bval_tools import (is_normalized_bvecs,
+                                              round_bvals_to_shell, normalize_bvecs)
+
+bvecs = np.asarray([[1.0, 1.0, 1.0],
+                    [1.0, 0.0, 1.0],
+                    [0.0, 1.0, 0.0]])
 
 
 def test_is_normalized_bvecs():
-    # toDO
-    pass
+    assert not is_normalized_bvecs(bvecs)
+    assert is_normalized_bvecs(
+        bvecs / np.linalg.norm(bvecs, axis=1, keepdims=True))
 
 
 def test_normalize_bvecs():
-    # toDo
-    pass
+    assert is_normalized_bvecs(normalize_bvecs(bvecs))
 
 
 def test_check_b0_threshold():

From 2e9c3b007f6fbe60a9ef3f7aabec8bda136bb91d Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Tue, 23 Jan 2024 14:11:40 -0500
Subject: [PATCH 62/97] mrtrix2fsl and fsl2mrtrix: Moved to io.gradients. They
 load and save.

---
 scilpy/gradients/bvec_bval_tools.py           | 72 -------------------
 .../gradients/tests/test_bvec_bval_tools.py   | 17 ++---
 scilpy/io/gradients.py                        | 63 ++++++++++++++++
 scripts/scil_NODDI_maps.py                    |  3 +-
 scripts/scil_freewater_maps.py                |  3 +-
 scripts/scil_gradients_convert.py             |  2 +-
 scripts/scil_tractogram_commit.py             |  3 +-
 7 files changed, 74 insertions(+), 89 deletions(-)

diff --git a/scilpy/gradients/bvec_bval_tools.py b/scilpy/gradients/bvec_bval_tools.py
index 8893fa1e1..c0fadebe4 100644
--- a/scilpy/gradients/bvec_bval_tools.py
+++ b/scilpy/gradients/bvec_bval_tools.py
@@ -6,9 +6,6 @@
 from dipy.core.gradients import get_bval_indices
 import numpy as np
 
-from scilpy.io.gradients import (save_gradient_sampling_fsl,
-                                 save_gradient_sampling_mrtrix)
-
 DEFAULT_B0_THRESHOLD = 20
 
 
@@ -114,75 +111,6 @@ def check_b0_threshold(
     return b0_thr
 
 
-def fsl2mrtrix(fsl_bval_filename, fsl_bvec_filename, mrtrix_filename):
-    """
-    Convert a fsl dir_grad.bvec/.bval files to mrtrix encoding.b file.
-
-    Parameters
-    ----------
-    fsl_bval_filename: str
-        path to input fsl bval file.
-    fsl_bvec_filename: str
-        path to input fsl bvec file.
-    mrtrix_filename : str
-        path to output mrtrix encoding.b file.
-
-    Returns
-    -------
-    """
-
-    shells = np.loadtxt(fsl_bval_filename)
-    points = np.loadtxt(fsl_bvec_filename)
-    bvals = np.unique(shells).tolist()
-
-    # Remove .bval and .bvec if present
-    mrtrix_filename = mrtrix_filename.replace('.b', '')
-
-    if not points.shape[0] == 3:
-        points = points.transpose()
-        logging.warning('WARNING: Your bvecs seem transposed. ' +
-                        'Transposing them.')
-
-    shell_idx = [int(np.where(bval == bvals)[0]) for bval in shells]
-    save_gradient_sampling_mrtrix(points,
-                                  shell_idx,
-                                  bvals,
-                                  mrtrix_filename + '.b')
-
-
-def mrtrix2fsl(mrtrix_filename, fsl_filename):
-    """
-    Convert a mrtrix encoding.b file to fsl dir_grad.bvec/.bval files.
-
-    Parameters
-    ----------
-    mrtrix_filename : str
-        path to mrtrix encoding.b file.
-    fsl_bval_filename: str
-        path to the output fsl files. Files will be named
-        fsl_bval_filename.bval and fsl_bval_filename.bvec.
-    """
-    # Remove .bval and .bvec if present
-    fsl_filename = fsl_filename.replace('.bval', '')
-    fsl_filename = fsl_filename.replace('.bvec', '')
-
-    mrtrix_b = np.loadtxt(mrtrix_filename)
-    if not len(mrtrix_b.shape) == 2 or not mrtrix_b.shape[1] == 4:
-        raise ValueError('mrtrix file must have 4 columns')
-
-    points = np.array([mrtrix_b[:, 0], mrtrix_b[:, 1], mrtrix_b[:, 2]])
-    shells = np.array(mrtrix_b[:, 3])
-
-    bvals = np.unique(shells).tolist()
-    shell_idx = [int(np.where(bval == bvals)[0]) for bval in shells]
-
-    save_gradient_sampling_fsl(points,
-                               shell_idx,
-                               bvals,
-                               filename_bval=fsl_filename + '.bval',
-                               filename_bvec=fsl_filename + '.bvec')
-
-
 def identify_shells(bvals, threshold=40.0, roundCentroids=False, sort=False):
     """
     Guessing the shells from the b-values. Returns the list of shells and, for
diff --git a/scilpy/gradients/tests/test_bvec_bval_tools.py b/scilpy/gradients/tests/test_bvec_bval_tools.py
index 5f0db7498..f23ce19e0 100644
--- a/scilpy/gradients/tests/test_bvec_bval_tools.py
+++ b/scilpy/gradients/tests/test_bvec_bval_tools.py
@@ -1,8 +1,9 @@
 # -*- coding: utf-8 -*-
 import numpy as np
 
-from scilpy.gradients.bvec_bval_tools import (is_normalized_bvecs,
-                                              round_bvals_to_shell, normalize_bvecs)
+from scilpy.gradients.bvec_bval_tools import (
+    check_b0_threshold, is_normalized_bvecs, normalize_bvecs,
+    round_bvals_to_shell)
 
 bvecs = np.asarray([[1.0, 1.0, 1.0],
                     [1.0, 0.0, 1.0],
@@ -20,17 +21,7 @@ def test_normalize_bvecs():
 
 
 def test_check_b0_threshold():
-    # toDo
-    pass
-
-
-def test_fsl2mrtrix():
-    # toDo
-    pass
-
-
-def test_mrtrix2fsl():
-    # toDo
+    # toDo To be modified (see PR#867).
     pass
 
 
diff --git a/scilpy/io/gradients.py b/scilpy/io/gradients.py
index 3c168c2e7..c72103e61 100644
--- a/scilpy/io/gradients.py
+++ b/scilpy/io/gradients.py
@@ -6,6 +6,69 @@
 import numpy as np
 
 
+def fsl2mrtrix(fsl_bval_filename, fsl_bvec_filename, mrtrix_filename):
+    """
+    Convert a fsl dir_grad.bvec/.bval files to mrtrix encoding.b file.
+    Saves the result.
+
+    Parameters
+    ----------
+    fsl_bval_filename: str
+        path to input fsl bval file.
+    fsl_bvec_filename: str
+        path to input fsl bvec file.
+    mrtrix_filename : str
+        path to output mrtrix encoding.b file.
+    """
+    shells = np.loadtxt(fsl_bval_filename)
+    points = np.loadtxt(fsl_bvec_filename)
+    bvals = np.unique(shells).tolist()
+
+    # Remove .bval and .bvec if present
+    mrtrix_filename = mrtrix_filename.replace('.b', '')
+
+    if not points.shape[0] == 3:
+        points = points.transpose()
+        logging.warning('WARNING: Your bvecs seem transposed. ' +
+                        'Transposing them.')
+
+    shell_idx = [int(np.where(bval == bvals)[0]) for bval in shells]
+    save_gradient_sampling_mrtrix(points, shell_idx, bvals,
+                                  mrtrix_filename + '.b')
+
+
+def mrtrix2fsl(mrtrix_filename, fsl_filename):
+    """
+    Convert a mrtrix encoding.b file to fsl dir_grad.bvec/.bval files.
+    Saves the result.
+
+    Parameters
+    ----------
+    mrtrix_filename : str
+        path to mrtrix encoding.b file.
+    fsl_filename: str
+        path to the output fsl files. Files will be named
+        fsl_bval_filename.bval and fsl_bval_filename.bvec.
+    """
+    # Remove .bval and .bvec if present
+    fsl_filename = fsl_filename.replace('.bval', '')
+    fsl_filename = fsl_filename.replace('.bvec', '')
+
+    mrtrix_b = np.loadtxt(mrtrix_filename)
+    if not len(mrtrix_b.shape) == 2 or not mrtrix_b.shape[1] == 4:
+        raise ValueError('mrtrix file must have 4 columns')
+
+    points = np.array([mrtrix_b[:, 0], mrtrix_b[:, 1], mrtrix_b[:, 2]])
+    shells = np.array(mrtrix_b[:, 3])
+
+    bvals = np.unique(shells).tolist()
+    shell_idx = [int(np.where(bval == bvals)[0]) for bval in shells]
+
+    save_gradient_sampling_fsl(points, shell_idx, bvals,
+                               filename_bval=fsl_filename + '.bval',
+                               filename_bvec=fsl_filename + '.bvec')
+
+
 def save_gradient_sampling_mrtrix(bvecs, shell_idx, bvals, filename):
     """
     Save table gradient (MRtrix format)
diff --git a/scripts/scil_NODDI_maps.py b/scripts/scil_NODDI_maps.py
index bb720a85c..b2d890bf8 100755
--- a/scripts/scil_NODDI_maps.py
+++ b/scripts/scil_NODDI_maps.py
@@ -20,13 +20,14 @@
 from dipy.io.gradients import read_bvals_bvecs
 import numpy as np
 
+from scilpy.io.gradients import fsl2mrtrix
 from scilpy.io.utils import (add_overwrite_arg,
                              add_processes_arg,
                              add_verbose_arg,
                              assert_inputs_exist,
                              assert_output_dirs_exist_and_empty,
                              redirect_stdout_c)
-from scilpy.gradients.bvec_bval_tools import fsl2mrtrix, identify_shells
+from scilpy.gradients.bvec_bval_tools import identify_shells
 
 EPILOG = """
 Reference:
diff --git a/scripts/scil_freewater_maps.py b/scripts/scil_freewater_maps.py
index b3fb44ba6..643c75380 100755
--- a/scripts/scil_freewater_maps.py
+++ b/scripts/scil_freewater_maps.py
@@ -20,13 +20,14 @@
 from dipy.io.gradients import read_bvals_bvecs
 import numpy as np
 
+from scilpy.io.gradients import fsl2mrtrix
 from scilpy.io.utils import (add_overwrite_arg,
                              add_processes_arg,
                              add_verbose_arg,
                              assert_inputs_exist,
                              assert_output_dirs_exist_and_empty,
                              redirect_stdout_c)
-from scilpy.gradients.bvec_bval_tools import fsl2mrtrix, identify_shells
+from scilpy.gradients.bvec_bval_tools import identify_shells
 
 
 EPILOG = """
diff --git a/scripts/scil_gradients_convert.py b/scripts/scil_gradients_convert.py
index f3cfd0025..f2c2d2766 100755
--- a/scripts/scil_gradients_convert.py
+++ b/scripts/scil_gradients_convert.py
@@ -14,7 +14,7 @@
 from scilpy.io.utils import (assert_gradients_filenames_valid,
                              assert_inputs_exist, assert_outputs_exist,
                              add_overwrite_arg, add_verbose_arg)
-from scilpy.gradients.bvec_bval_tools import fsl2mrtrix, mrtrix2fsl
+from scilpy.io.gradients import fsl2mrtrix, mrtrix2fsl
 
 
 def _build_arg_parser():
diff --git a/scripts/scil_tractogram_commit.py b/scripts/scil_tractogram_commit.py
index 736a62229..b52c6b36b 100755
--- a/scripts/scil_tractogram_commit.py
+++ b/scripts/scil_tractogram_commit.py
@@ -84,6 +84,7 @@
 import numpy as np
 import nibabel as nib
 
+from scilpy.io.gradients import fsl2mrtrix
 from scilpy.io.streamlines import (reconstruct_streamlines,
                                    reconstruct_streamlines_from_hdf5)
 from scilpy.io.utils import (add_overwrite_arg,
@@ -92,7 +93,7 @@
                              assert_inputs_exist,
                              assert_output_dirs_exist_and_empty,
                              redirect_stdout_c)
-from scilpy.gradients.bvec_bval_tools import fsl2mrtrix, identify_shells
+from scilpy.gradients.bvec_bval_tools import identify_shells
 
 
 EPILOG = """

From 21edbd31ff5746b8de79690fdb2294a5b5fea0c1 Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Tue, 23 Jan 2024 14:52:14 -0500
Subject: [PATCH 63/97] Test identify_shells. Added a warning. Renamed tol

---
 scilpy/gradients/bvec_bval_tools.py           | 29 ++++++++++-----
 .../gradients/tests/test_bvec_bval_tools.py   | 37 +++++++++++++++++--
 scilpy/image/volume_operations.py             |  4 +-
 scripts/scil_NODDI_maps.py                    |  2 +-
 scripts/scil_freewater_maps.py                |  2 +-
 scripts/scil_tractogram_commit.py             |  2 +-
 6 files changed, 58 insertions(+), 18 deletions(-)

diff --git a/scilpy/gradients/bvec_bval_tools.py b/scilpy/gradients/bvec_bval_tools.py
index c0fadebe4..252fd9d74 100644
--- a/scilpy/gradients/bvec_bval_tools.py
+++ b/scilpy/gradients/bvec_bval_tools.py
@@ -111,7 +111,7 @@ def check_b0_threshold(
     return b0_thr
 
 
-def identify_shells(bvals, threshold=40.0, roundCentroids=False, sort=False):
+def identify_shells(bvals, tol=40.0, round_centroids=False, sort=False):
     """
     Guessing the shells from the b-values. Returns the list of shells and, for
     each b-value, the associated shell.
@@ -128,10 +128,11 @@ def identify_shells(bvals, threshold=40.0, roundCentroids=False, sort=False):
     ----------
     bvals: array (N,)
         Array of bvals
-    threshold: float
-        Limit value to consider that a b-value is on an existing shell. Above
-        this limit, the b-value is placed on a new shell.
-    roundCentroids: bool
+    tol: float
+        Limit difference to centroid to consider that a b-value is on an
+        existing shell. On or above this limit, the b-value is placed on a new
+        shell.
+    round_centroids: bool
         If true will round shell values to the nearest 10.
     sort: bool
         Sort centroids and shell_indices associated.
@@ -151,7 +152,7 @@ def identify_shells(bvals, threshold=40.0, roundCentroids=False, sort=False):
     bval_centroids = [bvals[0]]
     for bval in bvals[1:]:
         diffs = np.abs(np.asarray(bval_centroids, dtype=float) - bval)
-        if not len(np.where(diffs < threshold)[0]):
+        if not len(np.where(diffs < tol)[0]):
             # Found no bval in bval centroids close enough to the current one.
             # Create new centroid (i.e. new shell)
             bval_centroids.append(bval)
@@ -163,15 +164,23 @@ def identify_shells(bvals, threshold=40.0, roundCentroids=False, sort=False):
 
     shell_indices = np.argmin(np.abs(bvals_for_diffs - centroids), axis=1)
 
-    if roundCentroids:
+    if round_centroids:
         centroids = np.round(centroids, decimals=-1)
 
+        # Ex: with bvals [0, 5], threshold 5, we get centroids 0, 5.
+        # Rounded, we get centroids 0, 0.
+        if len(np.unique(centroids)) != len(centroids):
+            logging.warning("With option to round the centroids to the "
+                            "nearest 10, with tolerance {}, we get unclear "
+                            "division of the shells. Use this data carefully."
+                            .format(tol))
+
     if sort:
         sort_index = np.argsort(centroids)
-        sorted_centroids = np.zeros(centroids.shape)
-        sorted_indices = np.zeros(shell_indices.shape)
+        sorted_centroids = centroids[sort_index]
+
+        sorted_indices = np.zeros(shell_indices.shape, dtype=int)
         for i in range(len(centroids)):
-            sorted_centroids[i] = centroids[sort_index[i]]
             sorted_indices[shell_indices == i] = sort_index[i]
         return sorted_centroids, sorted_indices
 
diff --git a/scilpy/gradients/tests/test_bvec_bval_tools.py b/scilpy/gradients/tests/test_bvec_bval_tools.py
index f23ce19e0..2f900fd78 100644
--- a/scilpy/gradients/tests/test_bvec_bval_tools.py
+++ b/scilpy/gradients/tests/test_bvec_bval_tools.py
@@ -3,7 +3,7 @@
 
 from scilpy.gradients.bvec_bval_tools import (
     check_b0_threshold, is_normalized_bvecs, normalize_bvecs,
-    round_bvals_to_shell)
+    round_bvals_to_shell, identify_shells)
 
 bvecs = np.asarray([[1.0, 1.0, 1.0],
                     [1.0, 0.0, 1.0],
@@ -26,8 +26,39 @@ def test_check_b0_threshold():
 
 
 def test_identify_shells():
-    # toDo
-    pass
+    def _subtest_identify_shells(bvals, threshold,
+                                 expected_raw_centroids, expected_raw_shells,
+                                 expected_round_sorted_centroids,
+                                 expected_round_sorted_shells):
+        bvals = np.asarray(bvals)
+
+        # 1) Not rounded, not sorted
+        c, s = identify_shells(bvals, threshold)
+        assert np.array_equal(c, expected_raw_centroids)
+        assert np.array_equal(s, expected_raw_shells)
+
+        # 2) Rounded, sorted
+        c, s = identify_shells(bvals, threshold, round_centroids=True,
+                               sort=True)
+        assert np.array_equal(c, expected_round_sorted_centroids)
+        assert np.array_equal(s, expected_round_sorted_shells)
+
+    # Test 1. All easy. Over the limit for 0, 5, 15. Clear difference for
+    # 100, 2000.
+    _subtest_identify_shells(bvals=[0, 0, 5, 15, 2000, 100], threshold=50,
+                             expected_raw_centroids=[0, 2000, 100],
+                             expected_raw_shells=[0, 0, 0, 0, 1, 2],
+                             expected_round_sorted_centroids=[0, 100, 2000],
+                             expected_round_sorted_shells=[0, 0, 0, 0, 2, 1])
+
+    # Test 2. Threshold on the limit.
+    # Additional difficulty with option rounded: two shells with the same
+    # value, but a warning is printed. Should it raise an error?
+    _subtest_identify_shells(bvals=[0, 0, 5, 2000, 100], threshold=5,
+                             expected_raw_centroids=[0, 5, 2000, 100],
+                             expected_raw_shells=[0, 0, 1, 2, 3],
+                             expected_round_sorted_centroids=[0, 0, 100, 2000],
+                             expected_round_sorted_shells=[0, 0, 1, 3, 2])
 
 
 def test_str_to_axis_index():
diff --git a/scilpy/image/volume_operations.py b/scilpy/image/volume_operations.py
index 463c39c8d..16fd8b04f 100644
--- a/scilpy/image/volume_operations.py
+++ b/scilpy/image/volume_operations.py
@@ -279,8 +279,8 @@ def compute_snr(dwi, bval, bvec, b0_thr, mask,
     mask = get_data_as_mask(mask, dtype=bool)
 
     if split_shells:
-        centroids, shell_indices = identify_shells(bval, threshold=40.0,
-                                                   roundCentroids=False,
+        centroids, shell_indices = identify_shells(bval, tol=40.0,
+                                                   round_centroids=False,
                                                    sort=False)
         bval = centroids[shell_indices]
 
diff --git a/scripts/scil_NODDI_maps.py b/scripts/scil_NODDI_maps.py
index b2d890bf8..82b12e40a 100755
--- a/scripts/scil_NODDI_maps.py
+++ b/scripts/scil_NODDI_maps.py
@@ -119,7 +119,7 @@ def main():
     bvals, _ = read_bvals_bvecs(args.in_bval, args.in_bvec)
     shells_centroids, indices_shells = identify_shells(bvals,
                                                        args.b_thr,
-                                                       roundCentroids=True)
+                                                       round_centroids=True)
     np.savetxt(tmp_bval_filename, shells_centroids[indices_shells],
                newline=' ', fmt='%i')
     fsl2mrtrix(tmp_bval_filename, args.in_bvec, tmp_scheme_filename)
diff --git a/scripts/scil_freewater_maps.py b/scripts/scil_freewater_maps.py
index 643c75380..7e108148a 100755
--- a/scripts/scil_freewater_maps.py
+++ b/scripts/scil_freewater_maps.py
@@ -126,7 +126,7 @@ def main():
     bvals, _ = read_bvals_bvecs(args.in_bval, args.in_bvec)
     shells_centroids, indices_shells = identify_shells(bvals,
                                                        args.b_thr,
-                                                       roundCentroids=True)
+                                                       round_centroids=True)
     np.savetxt(tmp_bval_filename, shells_centroids[indices_shells],
                newline=' ', fmt='%i')
     fsl2mrtrix(tmp_bval_filename, args.in_bvec, tmp_scheme_filename)
diff --git a/scripts/scil_tractogram_commit.py b/scripts/scil_tractogram_commit.py
index b52c6b36b..f03b9aba2 100755
--- a/scripts/scil_tractogram_commit.py
+++ b/scripts/scil_tractogram_commit.py
@@ -385,7 +385,7 @@ def main():
     tmp_bval_filename = os.path.join(tmp_dir.name, 'bval')
     bvals, _ = read_bvals_bvecs(args.in_bval, args.in_bvec)
     shells_centroids, indices_shells = identify_shells(bvals, args.b_thr,
-                                                       roundCentroids=True)
+                                                       round_centroids=True)
     np.savetxt(tmp_bval_filename, shells_centroids[indices_shells],
                newline=' ', fmt='%i')
     fsl2mrtrix(tmp_bval_filename, args.in_bvec, tmp_scheme_filename)

From 514e277ada99063710789d6cecdda34572c9ee00 Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Tue, 23 Jan 2024 15:02:21 -0500
Subject: [PATCH 64/97] Add test flip and swap axis

---
 scilpy/gradients/bvec_bval_tools.py           | 21 +++++++++-------
 .../gradients/tests/test_bvec_bval_tools.py   | 25 +++++++++++++------
 scripts/scil_gradients_modify_axes.py         | 12 ++++++++-
 3 files changed, 41 insertions(+), 17 deletions(-)

diff --git a/scilpy/gradients/bvec_bval_tools.py b/scilpy/gradients/bvec_bval_tools.py
index 252fd9d74..1f99d95a1 100644
--- a/scilpy/gradients/bvec_bval_tools.py
+++ b/scilpy/gradients/bvec_bval_tools.py
@@ -28,7 +28,6 @@ def is_normalized_bvecs(bvecs):
     -------
     True/False
     """
-
     bvecs_norm = np.linalg.norm(bvecs, axis=1)
     return np.all(np.logical_or(np.abs(bvecs_norm - 1) < 1e-3,
                                 bvecs_norm == 0))
@@ -48,7 +47,7 @@ def normalize_bvecs(bvecs):
     bvecs : (N, 3)
        normalized b-vectors
     """
-
+    bvecs = bvecs.copy()  # Avoid in-place modification.
     bvecs_norm = np.linalg.norm(bvecs, axis=1)
     idx = bvecs_norm != 0
     bvecs[idx] /= bvecs_norm[idx, None]
@@ -217,12 +216,13 @@ def flip_gradient_sampling(bvecs, axes, sampling_type):
     Parameters
     ----------
     bvecs: np.ndarray
-        Loaded bvecs. In the case 'mrtrix' the bvecs actually also contain the
-        bvals.
+        bvecs loaded directly, not re-formatted. Careful! Must respect the
+        format (not verified here).
     axes: list of int
-        List of axes to flip (e.g. [0, 1])
+        List of axes to flip (e.g. [0, 1]). See str_to_axis_index.
     sampling_type: str
-        Either 'mrtrix' or 'fsl'.
+        Either 'mrtrix': bvecs are of shape (N, 4) or
+               'fsl': bvecs are of shape (3, N)
 
     Returns
     -------
@@ -230,6 +230,8 @@ def flip_gradient_sampling(bvecs, axes, sampling_type):
         The final bvecs.
     """
     assert sampling_type in ['mrtrix', 'fsl']
+
+    bvecs = bvecs.copy()  # Avoid in-place modification.
     if sampling_type == 'mrtrix':
         for axis in axes:
             bvecs[:, axis] *= -1
@@ -246,12 +248,13 @@ def swap_gradient_axis(bvecs, final_order, sampling_type):
     Parameters
     ----------
     bvecs: np.array
-        Loaded bvecs. In the case 'mrtrix' the bvecs actually also contain the
-        bvals.
+        bvecs loaded directly, not re-formatted. Careful! Must respect the
+        format (not verified here).
     final_order: new order
         Final order (ex, 2 1 0)
     sampling_type: str
-        Either 'mrtrix' or 'fsl'.
+        Either 'mrtrix': bvecs are of shape (N, 4) or
+               'fsl': bvecs are of shape (3, N)
 
     Returns
     -------
diff --git a/scilpy/gradients/tests/test_bvec_bval_tools.py b/scilpy/gradients/tests/test_bvec_bval_tools.py
index 2f900fd78..64ef15f8f 100644
--- a/scilpy/gradients/tests/test_bvec_bval_tools.py
+++ b/scilpy/gradients/tests/test_bvec_bval_tools.py
@@ -3,11 +3,13 @@
 
 from scilpy.gradients.bvec_bval_tools import (
     check_b0_threshold, is_normalized_bvecs, normalize_bvecs,
-    round_bvals_to_shell, identify_shells)
+    round_bvals_to_shell, identify_shells, str_to_axis_index, flip_gradient_sampling,
+    swap_gradient_axis)
 
 bvecs = np.asarray([[1.0, 1.0, 1.0],
                     [1.0, 0.0, 1.0],
-                    [0.0, 1.0, 0.0]])
+                    [0.0, 1.0, 0.0],
+                    [8.0, 1.0, 1.0]])
 
 
 def test_is_normalized_bvecs():
@@ -63,17 +65,26 @@ def _subtest_identify_shells(bvals, threshold,
 
 def test_str_to_axis_index():
     # Very simple, nothing to do
-    pass
+    assert str_to_axis_index('x') == 0
 
 
 def test_flip_gradient_sampling():
-    # toDo
-    pass
+    fsl_bvecs = bvecs.T
+    b = flip_gradient_sampling(fsl_bvecs, axes=[0], sampling_type='fsl')
+    assert np.array_equal(b, np.asarray([[-1.0, 1.0, 1.0],
+                                         [-1.0, 0.0, 1.0],
+                                         [-0.0, 1.0, 0.0],
+                                         [-8.0, 1.0, 1.0]]).T)
 
 
 def test_swap_gradient_axis():
-    # toDo
-    pass
+    fsl_bvecs = bvecs.T
+    final_order = [1, 0, 2]
+    b = swap_gradient_axis(fsl_bvecs, final_order, sampling_type='fsl')
+    assert np.array_equal(b, np.asarray([[1.0, 1.0, 1.0],
+                                         [0.0, 1.0, 1.0],
+                                         [1.0, 0.0, 0.0],
+                                         [1.0, 8.0, 1.0]]).T)
 
 
 def test_round_bvals_to_shell():
diff --git a/scripts/scil_gradients_modify_axes.py b/scripts/scil_gradients_modify_axes.py
index 99f90c73f..a642725c6 100755
--- a/scripts/scil_gradients_modify_axes.py
+++ b/scripts/scil_gradients_modify_axes.py
@@ -83,14 +83,24 @@ def main():
     if len(np.unique(swapped_order)) != 3:
         parser.error("final_order should contain the three axis.")
 
+    # Could use io.gradients method, but we don't have a bvals file here, only
+    # treating with the bvecs. Loading directly.
     bvecs = np.loadtxt(args.in_gradient_sampling_file)
     if ext_in == '.bvec':
-        # Supposing FSL format
+        # Supposing FSL format: Per columns
+        if bvecs.shape[0] != 3:
+            parser.error("b-vectors format for a .b file should be FSL, "
+                         "and contain 3 lines (x, y, z), but got {}"
+                         .format(bvecs.shape[0]))
         bvecs = flip_gradient_sampling(bvecs, axes_to_flip, 'fsl')
         bvecs = swap_gradient_axis(bvecs, swapped_order, 'fsl')
         np.savetxt(args.out_gradient_sampling_file, bvecs, "%.8f")
     else:  # ext == '.b':
         # Supposing mrtrix format
+        if bvecs.shape[1] != 4:
+            parser.error("b-vectors format for a .b file should be mrtrix, "
+                         "and contain 4 columns (x, y, z, bval), but got {}"
+                         .format(bvecs.shape[1]))
         bvecs = flip_gradient_sampling(bvecs, axes_to_flip, 'mrtrix')
         bvecs = swap_gradient_axis(bvecs, swapped_order, 'mrtrix')
         np.savetxt(args.out_gradient_sampling_file, bvecs,

From 0d6e7a77b7ab8320919cb9fd589d23269b6bd3ab Mon Sep 17 00:00:00 2001
From: Emmanuelle Renauld <emmanuelle.renauld@usherbrooke.ca>
Date: Wed, 24 Jan 2024 15:40:25 -0500
Subject: [PATCH 65/97] Answer Arnaud's offline comment

---
 scilpy/gradients/tests/test_bvec_bval_tools.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/scilpy/gradients/tests/test_bvec_bval_tools.py b/scilpy/gradients/tests/test_bvec_bval_tools.py
index 64ef15f8f..3f413f3b1 100644
--- a/scilpy/gradients/tests/test_bvec_bval_tools.py
+++ b/scilpy/gradients/tests/test_bvec_bval_tools.py
@@ -66,6 +66,9 @@ def _subtest_identify_shells(bvals, threshold,
 def test_str_to_axis_index():
     # Very simple, nothing to do
     assert str_to_axis_index('x') == 0
+    assert str_to_axis_index('y') == 1
+    assert str_to_axis_index('z') == 2
+
 
 
 def test_flip_gradient_sampling():

From f0bc75a698be98b56ac4e555e673b068c570e29d Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Wed, 14 Feb 2024 10:14:02 -0500
Subject: [PATCH 66/97] Add test axis 'v' and fix pep8

---
 scilpy/gradients/tests/test_bvec_bval_tools.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/scilpy/gradients/tests/test_bvec_bval_tools.py b/scilpy/gradients/tests/test_bvec_bval_tools.py
index 3f413f3b1..3d82cc188 100644
--- a/scilpy/gradients/tests/test_bvec_bval_tools.py
+++ b/scilpy/gradients/tests/test_bvec_bval_tools.py
@@ -2,8 +2,8 @@
 import numpy as np
 
 from scilpy.gradients.bvec_bval_tools import (
-    check_b0_threshold, is_normalized_bvecs, normalize_bvecs,
-    round_bvals_to_shell, identify_shells, str_to_axis_index, flip_gradient_sampling,
+    identify_shells, is_normalized_bvecs, flip_gradient_sampling,
+    normalize_bvecs, round_bvals_to_shell, str_to_axis_index,
     swap_gradient_axis)
 
 bvecs = np.asarray([[1.0, 1.0, 1.0],
@@ -68,7 +68,7 @@ def test_str_to_axis_index():
     assert str_to_axis_index('x') == 0
     assert str_to_axis_index('y') == 1
     assert str_to_axis_index('z') == 2
-
+    assert str_to_axis_index('v') is None
 
 
 def test_flip_gradient_sampling():

From dedb657c5474c6fd4eca27734a12dec0dcf835e0 Mon Sep 17 00:00:00 2001
From: karp2601 <karp2601@dinf-0051-20b.DInf.fsci.usherbrooke.ca>
Date: Wed, 14 Feb 2024 11:49:19 -0500
Subject: [PATCH 67/97] Fixing pep8

---
 scripts/scil_frf_set_diffusivities.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/scil_frf_set_diffusivities.py b/scripts/scil_frf_set_diffusivities.py
index dbec3dbec..be564e3af 100755
--- a/scripts/scil_frf_set_diffusivities.py
+++ b/scripts/scil_frf_set_diffusivities.py
@@ -40,10 +40,10 @@ def _build_arg_parser():
                    help='If supplied, the fiber response function is\n'
                         'evaluated without the x 10**-4 factor. [%(default)s].'
                    )
-    
+
     add_verbose_arg(p)
     add_overwrite_arg(p)
-    
+
     return p
 
 

From 1cf2a0f937134599f5f98b0a44b4659bf15f5383 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Wed, 14 Feb 2024 14:57:19 -0500
Subject: [PATCH 68/97] disable test run on forks

---
 .github/workflows/test.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 082d54c0a..740cf4692 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -19,9 +19,10 @@ env:
 jobs:
   test:
     runs-on: scilus-runners
+    if: github.repository == 'scilus/scilpy'
     steps:
       - name: Checkout repository for merge
-        uses: actions/checkout@v4.1.1
+        uses: actions/checkout@v4
 
       - name: Fetch python version from repository
         id: python-selector

From a7952308d2aed5060fbb108202981d3bad9e9734 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Thu, 15 Feb 2024 12:59:31 -0500
Subject: [PATCH 69/97] write sources relative to repository

---
 .coveragerc | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.coveragerc b/.coveragerc
index 10530e8c5..e748ff743 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -2,6 +2,7 @@
 branch = True
 concurrency = multiprocessing
 data_file = .test_reports/.coverage
+relative_files = True
 source =
     scilpy/
     scripts/

From 62c678841c08db98445352a6e0a71984b3ea6560 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Thu, 15 Feb 2024 13:01:24 -0500
Subject: [PATCH 70/97] first try running only simple fast test to test upload
 and effect on codecov.io

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 740cf4692..9273974b6 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -53,7 +53,7 @@ jobs:
       - name: Run tests
         run: |
           export C_INCLUDE_PATH=$pythonLocation/include/python${{ steps.python-selector.outputs.python-version }}:$C_INCLUDE_PATH
-          pytest --cov-report term-missing:skip-covered
+          pytest --cov-report term-missing:skip-covered scripts/tests/test_bids_validate.py
 
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v3

From 62e71e1500ff3860b3c1a9b18df2efac367a8c18 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Thu, 15 Feb 2024 13:19:07 -0500
Subject: [PATCH 71/97] switch back to v4, to see if they fixed something

---
 .github/workflows/test.yml | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 9273974b6..5fc18ec10 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -56,16 +56,15 @@ jobs:
           pytest --cov-report term-missing:skip-covered scripts/tests/test_bids_validate.py
 
       - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v3
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+        uses: codecov/codecov-action@v4
         with:
+          token: ${{ secrets.CODECOV_TOKEN }}
           flags: unittests
           name: scilpy-unittests-${{ github.run_id }}
           verbose: true
           directory: .test_reports/
           fail_ci_if_error: true
-          root_dir: $GITHUB_WORKSPACE/scilpy/
+          plugin: pycoverage
 
       - name: Upload test reports and coverage to artifacts
         uses: actions/upload-artifact@v4.3.1

From 964ab4a172e17eb0344e3d894b638cf287e0222b Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Thu, 15 Feb 2024 13:21:53 -0500
Subject: [PATCH 72/97] Add test files with empty tests

---
 scilpy/dwi/tests/__init__.py        | 0
 scilpy/dwi/tests/test_operations.py | 9 +++++++++
 scilpy/dwi/tests/test_utils.py      | 9 +++++++++
 3 files changed, 18 insertions(+)
 create mode 100644 scilpy/dwi/tests/__init__.py
 create mode 100644 scilpy/dwi/tests/test_operations.py
 create mode 100644 scilpy/dwi/tests/test_utils.py

diff --git a/scilpy/dwi/tests/__init__.py b/scilpy/dwi/tests/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/scilpy/dwi/tests/test_operations.py b/scilpy/dwi/tests/test_operations.py
new file mode 100644
index 000000000..91d7ccb02
--- /dev/null
+++ b/scilpy/dwi/tests/test_operations.py
@@ -0,0 +1,9 @@
+# -*- coding: utf-8 -*-
+
+
+def test_apply_bias_field():
+    pass
+
+
+def test_compute_dwi_attenuation():
+    pass
diff --git a/scilpy/dwi/tests/test_utils.py b/scilpy/dwi/tests/test_utils.py
new file mode 100644
index 000000000..f6b4d5d51
--- /dev/null
+++ b/scilpy/dwi/tests/test_utils.py
@@ -0,0 +1,9 @@
+# -*- coding: utf-8 -*-
+
+
+def test_extract_dwi_shell():
+    pass
+
+
+def test_extract_b0():
+    pass

From 09323a1de806ef97602eff71240f2b1cd32ffbbe Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Thu, 15 Feb 2024 13:35:50 -0500
Subject: [PATCH 73/97] use source pkgs instead of simple source

---
 .coveragerc | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.coveragerc b/.coveragerc
index e748ff743..9f2015df3 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -3,9 +3,9 @@ branch = True
 concurrency = multiprocessing
 data_file = .test_reports/.coverage
 relative_files = True
-source =
-    scilpy/
-    scripts/
+source_pkgs =
+    scilpy
+    scripts
 omit =
     scripts/tests/*.py
     scilpy/tests/**/*.py

From 4ac0ac309e1436cb553a90a17c988710bd46b376 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Thu, 15 Feb 2024 13:36:49 -0500
Subject: [PATCH 74/97] check reports before codecov run

---
 .github/workflows/test.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 5fc18ec10..7820777ff 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -55,6 +55,13 @@ jobs:
           export C_INCLUDE_PATH=$pythonLocation/include/python${{ steps.python-selector.outputs.python-version }}:$C_INCLUDE_PATH
           pytest --cov-report term-missing:skip-covered scripts/tests/test_bids_validate.py
 
+      - name: Upload test reports and coverage to artifacts before codecov
+        uses: actions/upload-artifact@v4.3.1
+        with:
+          name: test-reports-before
+          path: |
+            .test_reports/*
+
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v4
         with:

From 46ed33cc361023fd4a0f967c886af97a50aca326 Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Thu, 15 Feb 2024 13:48:23 -0500
Subject: [PATCH 75/97] Finish cleaning the main of dwi_ scripts, for eventual
 unit tests

---
 scilpy/dwi/operations.py                   | 87 ++++++++++++++++++++++
 scilpy/dwi/tests/test_operations.py        |  4 +
 scilpy/io/varian_fdf.py                    |  4 +-
 scripts/scil_dwi_detect_volume_outliers.py | 75 ++-----------------
 4 files changed, 100 insertions(+), 70 deletions(-)

diff --git a/scilpy/dwi/operations.py b/scilpy/dwi/operations.py
index 7d6546075..29249e062 100644
--- a/scilpy/dwi/operations.py
+++ b/scilpy/dwi/operations.py
@@ -1,6 +1,12 @@
 import logging
+import math
+import pprint
+
 import numpy as np
 
+from scilpy.gradients.bvec_bval_tools import identify_shells, \
+    round_bvals_to_shell, DEFAULT_B0_THRESHOLD
+
 
 def apply_bias_field(dwi_data, bias_field_data, mask_data):
     """
@@ -131,3 +137,84 @@ def compute_dwi_attenuation(dwi_weights: np.ndarray, b0: np.ndarray):
     dwi_attenuation[np.logical_not(np.isfinite(dwi_attenuation))] = 0.
 
     return dwi_attenuation
+
+
+def detect_volume_outliers(data, bvecs, bvals, std_scale, verbose,
+                           b0_thr=DEFAULT_B0_THRESHOLD):
+    """
+    Parameters
+    ----------
+    data: np.ndarray
+        The dwi data.
+    bvecs: np.ndarray
+        The bvecs
+    bvals: np.array
+        The b-values vector.
+    std_scale: float
+        How many deviation from the mean are required to be considered an
+        outlier.
+    verbose: bool
+        If True, print even more stuff.
+    b0_thr: float
+        Value below which b-values are considered as b0.
+    """
+    results_dict = {}
+    shells_to_extract = identify_shells(bvals, b0_thr, sort=True)[0]
+    bvals = round_bvals_to_shell(bvals, shells_to_extract)
+    for bval in shells_to_extract[shells_to_extract > b0_thr]:
+        shell_idx = np.where(bvals == bval)[0]
+        shell = bvecs[shell_idx]
+        results_dict[bval] = np.ones((len(shell), 3)) * -1
+        for i, vec in enumerate(shell):
+            if np.linalg.norm(vec) < 0.001:
+                continue
+
+            dot_product = np.clip(np.tensordot(shell, vec, axes=1), -1, 1)
+            angle = np.arccos(dot_product) * 180 / math.pi
+            angle[np.isnan(angle)] = 0
+            idx = np.argpartition(angle, 4).tolist()
+            idx.remove(i)
+
+            avg_angle = np.average(angle[idx[:3]])
+            corr = np.corrcoef([data[..., shell_idx[i]].ravel(),
+                                data[..., shell_idx[idx[0]]].ravel(),
+                                data[..., shell_idx[idx[1]]].ravel(),
+                                data[..., shell_idx[idx[2]]].ravel()])
+            results_dict[bval][i] = [shell_idx[i], avg_angle,
+                                     np.average(corr[0, 1:])]
+
+    for key in results_dict.keys():
+        avg_angle = np.round(np.average(results_dict[key][:, 1]), 4)
+        std_angle = np.round(np.std(results_dict[key][:, 1]), 4)
+
+        avg_corr = np.round(np.average(results_dict[key][:, 2]), 4)
+        std_corr = np.round(np.std(results_dict[key][:, 2]), 4)
+
+        outliers_angle = np.argwhere(
+            results_dict[key][:, 1] < avg_angle - (std_scale * std_angle))
+        outliers_corr = np.argwhere(
+            results_dict[key][:, 2] < avg_corr - (std_scale * std_corr))
+
+        print('Results for shell {} with {} directions:'
+              .format(key, len(results_dict[key])))
+        print('AVG and STD of angles: {} +/- {}'
+              .format(avg_angle, std_angle))
+        print('AVG and STD of correlations: {} +/- {}'
+              .format(avg_corr, std_corr))
+
+        if len(outliers_angle) or len(outliers_corr):
+            print('Possible outliers ({} STD below or above average):'
+                  .format(std_scale))
+            print('Outliers based on angle [position (4D), value]')
+            for i in outliers_angle:
+                print(results_dict[key][i, :][0][0:2])
+            print('Outliers based on correlation [position (4D), value]')
+            for i in outliers_corr:
+                print(results_dict[key][i, :][0][0::2])
+        else:
+            print('No outliers detected.')
+
+        if verbose:
+            print('Shell with b-value {}'.format(key))
+            pprint.pprint(results_dict[key])
+        print()
diff --git a/scilpy/dwi/tests/test_operations.py b/scilpy/dwi/tests/test_operations.py
index 91d7ccb02..7ea12e015 100644
--- a/scilpy/dwi/tests/test_operations.py
+++ b/scilpy/dwi/tests/test_operations.py
@@ -7,3 +7,7 @@ def test_apply_bias_field():
 
 def test_compute_dwi_attenuation():
     pass
+
+
+def test_detect_volume_outliers():
+    pass
diff --git a/scilpy/io/varian_fdf.py b/scilpy/io/varian_fdf.py
index 6deb6f546..7736d42a7 100644
--- a/scilpy/io/varian_fdf.py
+++ b/scilpy/io/varian_fdf.py
@@ -424,7 +424,9 @@ def correct_procpar_intensity(dwi_data, dwi_path, b0_path):
 
             P1 = 10**(Ldb/20)
     """
-
+    # Not really an io function: does not load and save! But it is the only
+    # method we have concerning varian_fdf. Kept here, as decided by guru
+    # Arnaud.
     dwi_gain = get_gain(dwi_path)
     b0_gain = get_gain(b0_path)
 
diff --git a/scripts/scil_dwi_detect_volume_outliers.py b/scripts/scil_dwi_detect_volume_outliers.py
index f32bbefce..c5af9833c 100755
--- a/scripts/scil_dwi_detect_volume_outliers.py
+++ b/scripts/scil_dwi_detect_volume_outliers.py
@@ -15,20 +15,16 @@
 """
 
 import argparse
-import pprint
 
 from dipy.io.gradients import read_bvals_bvecs
 import nibabel as nib
-import numpy as np
 
+from scilpy.dwi.operations import detect_volume_outliers
 from scilpy.io.utils import (assert_inputs_exist,
                              add_force_b0_arg,
                              add_verbose_arg)
 from scilpy.gradients.bvec_bval_tools import (check_b0_threshold,
-                                              identify_shells,
-                                              normalize_bvecs,
-                                              round_bvals_to_shell)
-import math
+                                              normalize_bvecs)
 
 
 def _build_arg_parser():
@@ -49,7 +45,7 @@ def _build_arg_parser():
                         'diffusion weighting. [%(default)s]')
     p.add_argument('--std_scale', type=float, default=2.0,
                    help='How many deviation from the mean are required to be '
-                        'considered an outliers. [%(default)s]')
+                        'considered an outlier. [%(default)s]')
 
     add_force_b0_arg(p)
     add_verbose_arg(p)
@@ -64,73 +60,14 @@ def main():
     assert_inputs_exist(parser, [args.in_dwi, args.in_bval, args.in_bvec])
 
     bvals, bvecs = read_bvals_bvecs(args.in_bval, args.in_bvec)
-    dwi = nib.load(args.in_dwi)
-    data = dwi.get_fdata()
+    data = nib.load(args.in_dwi).get_fdata()
 
     b0_thr = check_b0_threshold(args.force_b0_threshold,
                                 bvals.min(), args.b0_thr)
     bvecs = normalize_bvecs(bvecs)
 
-    results_dict = {}
-    shells_to_extract = identify_shells(bvals, b0_thr, sort=True)[0]
-    bvals = round_bvals_to_shell(bvals, shells_to_extract)
-    for bval in shells_to_extract[shells_to_extract > args.b0_thr]:
-        shell_idx = np.where(bvals == bval)[0]
-        shell = bvecs[shell_idx]
-        results_dict[bval] = np.ones((len(shell), 3)) * -1
-        for i, vec in enumerate(shell):
-            if np.linalg.norm(vec) < 0.001:
-                continue
-
-            dot_product = np.clip(np.tensordot(shell, vec, axes=1), -1, 1)
-            angle = np.arccos(dot_product) * 180 / math.pi
-            angle[np.isnan(angle)] = 0
-            idx = np.argpartition(angle, 4).tolist()
-            idx.remove(i)
-
-            avg_angle = np.average(angle[idx[:3]])
-            corr = np.corrcoef([data[..., shell_idx[i]].ravel(),
-                                data[..., shell_idx[idx[0]]].ravel(),
-                                data[..., shell_idx[idx[1]]].ravel(),
-                                data[..., shell_idx[idx[2]]].ravel()])
-            results_dict[bval][i] = [shell_idx[i], avg_angle,
-                                     np.average(corr[0, 1:])]
-
-    for key in results_dict.keys():
-        avg_angle = np.round(np.average(results_dict[key][:, 1]), 4)
-        std_angle = np.round(np.std(results_dict[key][:, 1]), 4)
-
-        avg_corr = np.round(np.average(results_dict[key][:, 2]), 4)
-        std_corr = np.round(np.std(results_dict[key][:, 2]), 4)
-
-        outliers_angle = np.argwhere(
-            results_dict[key][:, 1] < avg_angle-(args.std_scale*std_angle))
-        outliers_corr = np.argwhere(
-            results_dict[key][:, 2] < avg_corr-(args.std_scale*std_corr))
-
-        print('Results for shell {} with {} directions:'.format(
-            key, len(results_dict[key])))
-        print('AVG and STD of angles: {} +/- {}'.format(
-            avg_angle, std_angle))
-        print('AVG and STD of correlations: {} +/- {}'.format(
-            avg_corr, std_corr))
-
-        if len(outliers_angle) or len(outliers_corr):
-            print('Possible outliers ({} STD below or above average):'.format(
-                args.std_scale))
-            print('Outliers based on angle [position (4D), value]')
-            for i in outliers_angle:
-                print(results_dict[key][i, :][0][0:2])
-            print('Outliers based on correlation [position (4D), value]')
-            for i in outliers_corr:
-                print(results_dict[key][i, :][0][0::2])
-        else:
-            print('No outliers detected.')
-
-        if args.verbose:
-            print('Shell with b-value {}'.format(key))
-            pprint.pprint(results_dict[key])
-        print()
+    detect_volume_outliers(data, bvecs, bvals, args.std_scale,
+                           args.verbose, b0_thr)
 
 
 if __name__ == "__main__":

From a7bb40f485dc83c92cb5ad3ec44f7a35b680e697 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Thu, 15 Feb 2024 14:04:48 -0500
Subject: [PATCH 76/97] use master as ref for PRs

---
 .github/workflows/test.yml | 10 ++--------
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 7820777ff..4410cd296 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -53,14 +53,7 @@ jobs:
       - name: Run tests
         run: |
           export C_INCLUDE_PATH=$pythonLocation/include/python${{ steps.python-selector.outputs.python-version }}:$C_INCLUDE_PATH
-          pytest --cov-report term-missing:skip-covered scripts/tests/test_bids_validate.py
-
-      - name: Upload test reports and coverage to artifacts before codecov
-        uses: actions/upload-artifact@v4.3.1
-        with:
-          name: test-reports-before
-          path: |
-            .test_reports/*
+          pytest --cov-report term-missing:skip-covered
 
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v4
@@ -72,6 +65,7 @@ jobs:
           directory: .test_reports/
           fail_ci_if_error: true
           plugin: pycoverage
+          commit_parent: ${{ github.event.pull_request.base.sha || github.event.before }}
 
       - name: Upload test reports and coverage to artifacts
         uses: actions/upload-artifact@v4.3.1

From 6ae0976636b493d3ed9297fb11955e4e41440a17 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Thu, 15 Feb 2024 14:49:58 -0500
Subject: [PATCH 77/97] remove force base, as it breaks PR coverage counters

---
 .github/workflows/test.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 4410cd296..ff4f3bf28 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -65,7 +65,6 @@ jobs:
           directory: .test_reports/
           fail_ci_if_error: true
           plugin: pycoverage
-          commit_parent: ${{ github.event.pull_request.base.sha || github.event.before }}
 
       - name: Upload test reports and coverage to artifacts
         uses: actions/upload-artifact@v4.3.1

From 773ed7f098a78d86a231daf7b09d1889d53a2cf2 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Fri, 16 Feb 2024 16:14:25 -0500
Subject: [PATCH 78/97] update coveragerc

---
 .coveragerc | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/.coveragerc b/.coveragerc
index 9f2015df3..21b501e1c 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -1,11 +1,11 @@
 [run]
 branch = True
 concurrency = multiprocessing
-data_file = .test_reports/.coverage
-relative_files = True
-source_pkgs =
+data_file = .coverage
+source_pkgs = 
     scilpy
     scripts
+relative_files = True
 omit =
     scripts/tests/*.py
     scilpy/tests/**/*.py
@@ -16,6 +16,11 @@ omit =
 
 [report]
 skip_empty = True
+skip_covered = True
 
 [html]
 title = Scilpy Coverage Report
+directory = .test_reports/coverage.html
+
+[xml]
+output = .test_reports/coverage.xml

From d56551ee7f62033f2f9eae7209201480fe270716 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Fri, 16 Feb 2024 16:14:56 -0500
Subject: [PATCH 79/97] simplify pytest.ini

---
 pytest.ini | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/pytest.ini b/pytest.ini
index 5a7cbe175..b4b9224d1 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -33,8 +33,7 @@ junit_logging = out-err
 
 addopts =
     --html=.test_reports/pytest.html
-    --cov-report=html:.test_reports/coverage.html
     --junit-xml=.test_reports/junit.xml
-    --cov-report=xml:.test_reports/coverage.xml
-    --cov=scilpy/
-    --cov=scripts/    
+    --cov
+    --cov-report html
+    --cov-report xml

From 543d1c264b08b5567bf3d82aa5ddd65435706e03 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Fri, 16 Feb 2024 16:15:37 -0500
Subject: [PATCH 80/97] tests should now run

---
 .github/workflows/test.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index ff4f3bf28..ded929612 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -62,7 +62,6 @@ jobs:
           flags: unittests
           name: scilpy-unittests-${{ github.run_id }}
           verbose: true
-          directory: .test_reports/
           fail_ci_if_error: true
           plugin: pycoverage
 

From d0410dd9b7021d198a5861b3863aeb6cce92f18a Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 19 Feb 2024 10:19:08 -0500
Subject: [PATCH 81/97] remove unused StatefulTractogram

---
 scripts/scil_tractogram_project_map_to_streamlines.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/scil_tractogram_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
index 18d0a64ed..0f322b429 100755
--- a/scripts/scil_tractogram_project_map_to_streamlines.py
+++ b/scripts/scil_tractogram_project_map_to_streamlines.py
@@ -13,7 +13,7 @@
 import argparse
 import logging
 
-from dipy.io.streamline import save_tractogram, StatefulTractogram
+from dipy.io.streamline import save_tractogram
 
 from scilpy.io.image import load_img
 from scilpy.io.streamlines import load_tractogram_with_reference

From ced021733b06e935cd4de60d46556603ee9dc0c5 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 19 Feb 2024 10:19:59 -0500
Subject: [PATCH 82/97] removed extra spaces

---
 scripts/scil_tractogram_project_map_to_streamlines.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/scil_tractogram_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
index 0f322b429..5db45c336 100755
--- a/scripts/scil_tractogram_project_map_to_streamlines.py
+++ b/scripts/scil_tractogram_project_map_to_streamlines.py
@@ -51,8 +51,8 @@ def _build_arg_parser():
     p.add_argument('--endpoints_only', action='store_true',
                    help='If set, will only project the map onto the \n'
                    'endpoints of the streamlines (all other values along \n'
-                   ' streamlines will be NaN). If not set, will project \n'
-                   ' the map onto all points of the streamlines.')
+                   'streamlines will be NaN). If not set, will project \n'
+                   'the map onto all points of the streamlines.')
     p.add_argument('--overwrite_data', action='store_true', default=False,
                    help='If set, will overwrite data_per_point in the '
                    'output tractogram, otherwise previous data will be '

From 0c8e07b057d04f9ff950549e30011e17d3dc32a2 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 19 Feb 2024 10:20:25 -0500
Subject: [PATCH 83/97] removed default false

---
 scripts/scil_tractogram_project_map_to_streamlines.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/scil_tractogram_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
index 5db45c336..c41e55da7 100755
--- a/scripts/scil_tractogram_project_map_to_streamlines.py
+++ b/scripts/scil_tractogram_project_map_to_streamlines.py
@@ -53,7 +53,7 @@ def _build_arg_parser():
                    'endpoints of the streamlines (all other values along \n'
                    'streamlines will be NaN). If not set, will project \n'
                    'the map onto all points of the streamlines.')
-    p.add_argument('--overwrite_data', action='store_true', default=False,
+    p.add_argument('--overwrite_data', action='store_true',
                    help='If set, will overwrite data_per_point in the '
                    'output tractogram, otherwise previous data will be '
                    'preserved in the output tractogram.')

From e401f55886b59b95dbbd1ea4c931e4d691f6d1f1 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 19 Feb 2024 10:32:43 -0500
Subject: [PATCH 84/97] changed to nib.load

---
 ...l_tractogram_project_map_to_streamlines.py | 24 ++++++++++---------
 1 file changed, 13 insertions(+), 11 deletions(-)

diff --git a/scripts/scil_tractogram_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
index c41e55da7..9a5eeecfa 100755
--- a/scripts/scil_tractogram_project_map_to_streamlines.py
+++ b/scripts/scil_tractogram_project_map_to_streamlines.py
@@ -13,9 +13,9 @@
 import argparse
 import logging
 
+import nibabel as nib
 from dipy.io.streamline import save_tractogram
 
-from scilpy.io.image import load_img
 from scilpy.io.streamlines import load_tractogram_with_reference
 from scilpy.io.utils import (add_overwrite_arg,
                              add_reference_arg,
@@ -53,10 +53,15 @@ def _build_arg_parser():
                    'endpoints of the streamlines (all other values along \n'
                    'streamlines will be NaN). If not set, will project \n'
                    'the map onto all points of the streamlines.')
-    p.add_argument('--overwrite_data', action='store_true',
-                   help='If set, will overwrite data_per_point in the '
-                   'output tractogram, otherwise previous data will be '
-                   'preserved in the output tractogram.')
+
+    p.add_argument('--keep_all_dpp', action='store_true',
+                   help='If set, previous data_per_point will be preserved '
+                   'in the output tractogram. Else, only --out_dpp_name '
+                   'keys will be saved.')
+    p.add_argument('--overwrite_dpp', action='store_true', default=False,
+                   help='If set, if --keep_all_dpp is set and some --out_dpp_name '
+                   'keys already existed in your data_per_point, allow overwriting '
+                   'old data_per_point.')
 
     add_reference_arg(p)
     add_overwrite_arg(p)
@@ -102,7 +107,7 @@ def main():
     data_per_point = {}
     for fmap, dpp_name in zip(args.in_maps, args.out_dpp_name):
         logging.debug("Loading the map...")
-        map_img, map_dtype = load_img(fmap)
+        map_img = nib.load(fmap)
         map_data = map_img.get_fdata(caching='unchanged', dtype=float)
         map_res = map_img.header.get_zooms()[:3]
 
@@ -126,11 +131,8 @@ def main():
         out_sft = sft.from_sft(sft.streamlines, sft,
                                data_per_point=data_per_point)
     else:
-        old_data_per_point = sft.data_per_point
-        for dpp_name in data_per_point:
-            old_data_per_point[dpp_name] = data_per_point[dpp_name]
-        out_sft = sft.from_sft(sft.streamlines, sft,
-                               data_per_point=old_data_per_point)
+        sft.data_per_point.update(data_per_point)
+        out_sft = sft
 
     save_tractogram(out_sft, args.out_tractogram)
 

From 0f0abcce00ce25aa5989b2c865c8c819cffb2f0d Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 19 Feb 2024 10:57:42 -0500
Subject: [PATCH 85/97] added dual keep_dpp and ovewrite args

---
 scripts/scil_tractogram_project_map_to_streamlines.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/scripts/scil_tractogram_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
index 9a5eeecfa..9acea7f9f 100755
--- a/scripts/scil_tractogram_project_map_to_streamlines.py
+++ b/scripts/scil_tractogram_project_map_to_streamlines.py
@@ -58,7 +58,7 @@ def _build_arg_parser():
                    help='If set, previous data_per_point will be preserved '
                    'in the output tractogram. Else, only --out_dpp_name '
                    'keys will be saved.')
-    p.add_argument('--overwrite_dpp', action='store_true', default=False,
+    p.add_argument('--overwrite_dpp', action='store_true',
                    help='If set, if --keep_all_dpp is set and some --out_dpp_name '
                    'keys already existed in your data_per_point, allow overwriting '
                    'old data_per_point.')
@@ -127,12 +127,12 @@ def main():
 
         data_per_point[dpp_name] = streamline_data
 
-    if args.overwrite_data:
-        out_sft = sft.from_sft(sft.streamlines, sft,
-                               data_per_point=data_per_point)
-    else:
+    if args.keep_all_dpp:
         sft.data_per_point.update(data_per_point)
         out_sft = sft
+    else:
+        out_sft = sft.from_sft(sft.streamlines, sft,
+                               data_per_point=data_per_point)
 
     save_tractogram(out_sft, args.out_tractogram)
 

From 3fed0f1535f4f20729e89a9f8e6dea39f78b5f40 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 19 Feb 2024 11:01:22 -0500
Subject: [PATCH 86/97] changed map to map_volume

---
 scilpy/tractograms/dps_and_dpp_management.py  | 22 +++++++++----------
 ...l_tractogram_project_map_to_streamlines.py |  4 ++--
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/scilpy/tractograms/dps_and_dpp_management.py b/scilpy/tractograms/dps_and_dpp_management.py
index d919e4788..92cb3fb64 100644
--- a/scilpy/tractograms/dps_and_dpp_management.py
+++ b/scilpy/tractograms/dps_and_dpp_management.py
@@ -2,7 +2,7 @@
 import numpy as np
 
 
-def project_map_to_streamlines(sft, map, endpoints_only=False):
+def project_map_to_streamlines(sft, map_volume, endpoints_only=False):
     """
     Projects a map onto the points of streamlines.
 
@@ -10,36 +10,36 @@ def project_map_to_streamlines(sft, map, endpoints_only=False):
     ----------
     sft: StatefulTractogram
         Input tractogram.
-    map: DataVolume
+    map_volume: DataVolume
         Input map.
 
     Optional:
     ---------
     endpoints_only: bool
-        If True, will only project the map onto the endpoints of the
+        If True, will only project the map_volume onto the endpoints of the
         streamlines (all values along streamlines set to zero). If False,
-        will project the map onto all points of the streamlines.
+        will project the map_volume onto all points of the streamlines.
 
     Returns
     -------
     streamline_data:
-        map projected to each point of the streamlines.
+        map_volume projected to each point of the streamlines.
     """
-    if len(map.data.shape) == 4:
-        dimension = map.data.shape[3]
+    if len(map_volume.data.shape) == 4:
+        dimension = map_volume.data.shape[3]
     else:
         dimension = 1
 
     streamline_data = []
     if endpoints_only:
         for s in sft.streamlines:
-            p1_data = map.get_value_at_coordinate(
+            p1_data = map_volume.get_value_at_coordinate(
                 s[0][0], s[0][1], s[0][2],
                 space=sft.space, origin=sft.origin)
-            p2_data = map.get_value_at_coordinate(
+            p2_data = map_volume.get_value_at_coordinate(
                 s[-1][0], s[-1][1], s[-1][2],
                 space=sft.space, origin=sft.origin)
-            thisstreamline_data = []
+
             if dimension == 1:
                 thisstreamline_data = np.ones((len(s), 1)) * np.nan
             else:
@@ -57,7 +57,7 @@ def project_map_to_streamlines(sft, map, endpoints_only=False):
         for s in sft.streamlines:
             thisstreamline_data = []
             for p in s:
-                thisstreamline_data.append(map.get_value_at_coordinate(
+                thisstreamline_data.append(map_volume.get_value_at_coordinate(
                     p[0], p[1], p[2], space=sft.space, origin=sft.origin))
 
             streamline_data.append(
diff --git a/scripts/scil_tractogram_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
index 9acea7f9f..74468ccb0 100755
--- a/scripts/scil_tractogram_project_map_to_streamlines.py
+++ b/scripts/scil_tractogram_project_map_to_streamlines.py
@@ -116,11 +116,11 @@ def main():
         else:
             interp = "nearest"
 
-        map = DataVolume(map_data, map_res, interp)
+        map_volume = DataVolume(map_data, map_res, interp)
 
         logging.debug("Projecting map onto streamlines")
         streamline_data = project_map_to_streamlines(
-            sft, map,
+            sft, map_volume,
             endpoints_only=args.endpoints_only)
 
         logging.debug("Saving the tractogram...")

From 691c620c7e6fbed10dc37f5effa81bbba8de54b8 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 19 Feb 2024 11:06:25 -0500
Subject: [PATCH 87/97] updated logging in project_map

---
 scripts/scil_tractogram_project_map_to_streamlines.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/scripts/scil_tractogram_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
index 74468ccb0..7e8ad326c 100755
--- a/scripts/scil_tractogram_project_map_to_streamlines.py
+++ b/scripts/scil_tractogram_project_map_to_streamlines.py
@@ -77,7 +77,10 @@ def main():
 
     assert_outputs_exist(parser, args, [args.out_tractogram])
 
-    logging.debug("Loading the tractogram...")
+    if args.verbose:
+        logging.getLogger().setLevel(logging.INFO)
+
+    logging.info("Loading the tractogram...")
     sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
     sft.to_voxmm()
     sft.to_corner()
@@ -106,7 +109,7 @@ def main():
 
     data_per_point = {}
     for fmap, dpp_name in zip(args.in_maps, args.out_dpp_name):
-        logging.debug("Loading the map...")
+        logging.info("Loading the map...")
         map_img = nib.load(fmap)
         map_data = map_img.get_fdata(caching='unchanged', dtype=float)
         map_res = map_img.header.get_zooms()[:3]
@@ -118,12 +121,12 @@ def main():
 
         map_volume = DataVolume(map_data, map_res, interp)
 
-        logging.debug("Projecting map onto streamlines")
+        logging.info("Projecting map onto streamlines")
         streamline_data = project_map_to_streamlines(
             sft, map_volume,
             endpoints_only=args.endpoints_only)
 
-        logging.debug("Saving the tractogram...")
+        logging.info("Saving the tractogram...")
 
         data_per_point[dpp_name] = streamline_data
 

From 172e821f05f59689673a25b4d47290003540e2fb Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 19 Feb 2024 11:09:20 -0500
Subject: [PATCH 88/97] remove if statement

---
 scilpy/tractograms/dps_and_dpp_management.py          | 6 +-----
 scripts/scil_tractogram_project_map_to_streamlines.py | 5 +++++
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/scilpy/tractograms/dps_and_dpp_management.py b/scilpy/tractograms/dps_and_dpp_management.py
index 92cb3fb64..4fcdd8e21 100644
--- a/scilpy/tractograms/dps_and_dpp_management.py
+++ b/scilpy/tractograms/dps_and_dpp_management.py
@@ -40,11 +40,7 @@ def project_map_to_streamlines(sft, map_volume, endpoints_only=False):
                 s[-1][0], s[-1][1], s[-1][2],
                 space=sft.space, origin=sft.origin)
 
-            if dimension == 1:
-                thisstreamline_data = np.ones((len(s), 1)) * np.nan
-            else:
-                thisstreamline_data = np.ones(
-                    (len(s), p1_data.shape[0])) * np.nan
+            thisstreamline_data = np.ones((len(s), dimension)) * np.nan
 
             thisstreamline_data[0] = p1_data
             thisstreamline_data[-1] = p2_data
diff --git a/scripts/scil_tractogram_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
index 7e8ad326c..02fa59051 100755
--- a/scripts/scil_tractogram_project_map_to_streamlines.py
+++ b/scripts/scil_tractogram_project_map_to_streamlines.py
@@ -137,6 +137,11 @@ def main():
         out_sft = sft.from_sft(sft.streamlines, sft,
                                data_per_point=data_per_point)
 
+    print("New data_per_point keys are: ")
+    for key in args.out_dpp_name:
+        print("  - {} with shape per point {}"
+              .format(key, out_sft.data_per_point[key][0].shape[1:]))
+
     save_tractogram(out_sft, args.out_tractogram)
 
 

From d4c4f572fe03e783d3f7cfe03f1158c43224f767 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 19 Feb 2024 11:23:18 -0500
Subject: [PATCH 89/97] fixed comments in dpp_math

---
 scripts/scil_tractogram_dpp_math.py | 58 ++++++++++++++---------------
 1 file changed, 29 insertions(+), 29 deletions(-)

diff --git a/scripts/scil_tractogram_dpp_math.py b/scripts/scil_tractogram_dpp_math.py
index 12034bf8f..4cb7852fd 100755
--- a/scripts/scil_tractogram_dpp_math.py
+++ b/scripts/scil_tractogram_dpp_math.py
@@ -2,24 +2,24 @@
 # -*- coding: utf-8 -*-
 
 """
-Performs an operation on data per point from input streamlines.
-
-Two modes of operation are supported: data per streamline (dps) and data per
-point (dpp).
-
-In dps mode, the operation is performed across all dimensions of the data
-resulting in a single value per streamline.
-
-In dpp mode the operation is performed on each point separately, resulting in
-a single value per point.
-
-If endpoints_only and dpp mode is set operation will only
+Performs an operation on data per point (dpp) from input streamlines.
+
+Although the input data always comes from the dpp, the output can be either
+a dpp or a data_per_streamline (dps), depending on the chosen options.
+Two modes of operation are supported: dpp and dps.
+   - In dps mode, the operation is performed on dpp across the dimension of
+   the streamlines resulting in a single value (or array in the 4D case)
+   per streamline, stored as dps.
+   - In dpp mode, the operation is performed on each point separately, resulting in
+   a new dpp.
+
+If endpoints_only and dpp mode is set the operation will only
 be calculated at the streamline endpoints the rest of the
 values along the streamline will be NaN
 
 If endpoints_only and dps mode is set operation will be calculated
 across the data at the endpoints and stored as a
-single value per streamline.
+single value (or array in the 4D case) per streamline.
 
 Endpoint only operation:
 correlation: correlation calculated between arrays extracted from
@@ -53,31 +53,31 @@ def _build_arg_parser():
     p.add_argument('operation', metavar='OPERATION',
                    choices=['mean', 'sum', 'min',
                             'max', 'correlation'],
-                   help='The type of operation to be performed on the '
-                        'streamlines. Must\nbe one of the following: '
+                   help='The type of operation to be performed on the \n'
+                        'streamlines. Must\nbe one of the following: \n'
                         '%(choices)s.')
     p.add_argument('dpp_or_dps', metavar='DPP_OR_DPS',
                    choices=['dpp', 'dps'],
-                   help='Set to dps if the operation is to be performed '
-                   'across all dimensions resulting in a single value per '
-                   'streamline. Set to dpp if the operation is to be '
-                   'performed on each point separately resulting in a single '
+                   help='Set to dps if the operation is to be performed \n'
+                   'across all dimensions resulting in a single value per \n'
+                   'streamline. Set to dpp if the operation is to be \n'
+                   'performed on each point separately resulting in a single \n'
                    'value per point.')
     p.add_argument('in_tractogram', metavar='INPUT_FILE',
-                   help='Input tractogram containing streamlines and '
+                   help='Input tractogram containing streamlines and \n'
                         'metadata.')
     p.add_argument('--in_dpp_name',  nargs='+', required=True,
-                   help='Name or list of names of the data_per_point for '
-                        'operation to be performed on. If more than one dpp '
-                        'is selected, the same operation will be applied '
+                   help='Name or list of names of the data_per_point for \n'
+                        'operation to be performed on. If more than one dpp \n'
+                        'is selected, the same operation will be applied \n'
                         'separately to each one.')
     p.add_argument('--out_name', nargs='+', required=True,
-                   help='Name of the resulting data_per_point or '
-                   'data_per_streamline to be saved in the output '
-                   'tractogram. If more than one --in_dpp_name was used, '
+                   help='Name of the resulting data_per_point or \n'
+                   'data_per_streamline to be saved in the output \n'
+                   'tractogram. If more than one --in_dpp_name was used, \n'
                    'enter the same number of --out_name values.')
     p.add_argument('out_tractogram', metavar='OUTPUT_FILE',
-                   help='The file where the remaining streamlines '
+                   help='The file where the remaining streamlines \n'
                         'are saved.')
 
     p.add_argument('--endpoints_only', action='store_true', default=False,
@@ -85,8 +85,8 @@ def _build_arg_parser():
                    'If not set, will perform operation on all streamline \n'
                    'points.')
     p.add_argument('--overwrite_data', action='store_true', default=False,
-                   help='If set, will overwrite the data_per_point or '
-                   'data_per_streamline in the output tractogram, otherwise '
+                   help='If set, will overwrite the data_per_point or \n'
+                   'data_per_streamline in the output tractogram, otherwise \n'
                    'previous data will be preserved in the output tractogram.')
 
     add_reference_arg(p)

From 0a4966a17086299304e324b1d0c6c5defcc8d990 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 19 Feb 2024 11:34:55 -0500
Subject: [PATCH 90/97] updated to mode required argument

---
 scripts/scil_tractogram_dpp_math.py                   | 9 ++++-----
 scripts/scil_tractogram_project_map_to_streamlines.py | 2 +-
 scripts/tests/test_tractogram_dpp_math.py             | 4 ++--
 3 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/scripts/scil_tractogram_dpp_math.py b/scripts/scil_tractogram_dpp_math.py
index 4cb7852fd..fe01a0380 100755
--- a/scripts/scil_tractogram_dpp_math.py
+++ b/scripts/scil_tractogram_dpp_math.py
@@ -56,8 +56,7 @@ def _build_arg_parser():
                    help='The type of operation to be performed on the \n'
                         'streamlines. Must\nbe one of the following: \n'
                         '%(choices)s.')
-    p.add_argument('dpp_or_dps', metavar='DPP_OR_DPS',
-                   choices=['dpp', 'dps'],
+    p.add_argument('--mode', required=True, choices=['dpp', 'dps'],
                    help='Set to dps if the operation is to be performed \n'
                    'across all dimensions resulting in a single value per \n'
                    'streamline. Set to dpp if the operation is to be \n'
@@ -138,7 +137,7 @@ def main():
                          'point. Exiting.')
             return
 
-        if args.operation == 'correlation' and args.dpp_or_dps == 'dpp':
+        if args.operation == 'correlation' and args.mode == 'dpp':
             logging.info('Correlation operation requires dps mode. Exiting.')
             return
 
@@ -161,7 +160,7 @@ def main():
                 args.operation, sft, in_dpp_name)
 
             data_per_streamline[out_name] = new_dps
-        elif args.dpp_or_dps == 'dpp':
+        elif args.mode == 'dpp':
             # Results in new data per point
             logging.info(
                 'Performing {} on data from each streamine point '
@@ -170,7 +169,7 @@ def main():
             new_dpp = perform_streamline_operation_per_point(
                 args.operation, sft, in_dpp_name, args.endpoints_only)
             data_per_point[out_name] = new_dpp
-        elif args.dpp_or_dps == 'dps':
+        elif args.mode == 'dps':
             # Results in new data per streamline
             logging.info(
                 'Performing {} across each streamline and saving resulting '
diff --git a/scripts/scil_tractogram_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
index 02fa59051..e7578a80b 100755
--- a/scripts/scil_tractogram_project_map_to_streamlines.py
+++ b/scripts/scil_tractogram_project_map_to_streamlines.py
@@ -99,7 +99,7 @@ def main():
         parser.error('The output names (out_dpp_names) must be unique.')
 
     # Check to see if the output names already exist in the input tractogram
-    if not args.overwrite_data:
+    if not args.overwrite_dpp:
         for out_dpp_name in args.out_dpp_name:
             if out_dpp_name in sft.data_per_point:
                 logging.info('out_name {} already exists in input tractogram. '
diff --git a/scripts/tests/test_tractogram_dpp_math.py b/scripts/tests/test_tractogram_dpp_math.py
index ef89d6eca..69387b53d 100644
--- a/scripts/tests/test_tractogram_dpp_math.py
+++ b/scripts/tests/test_tractogram_dpp_math.py
@@ -34,9 +34,9 @@ def test_execution_tractogram_point_math_mean_3D_defaults(script_runner):
 
     ret = script_runner.run('scil_tractogram_dpp_math.py',
                             'mean',
-                            'dps',
                             t1_on_bundle,
                             't1_mean_on_streamlines.trk',
+                            '--mode', 'dps',
                             '--in_dpp_name', 't1',
                             '--out_name', 't1_mean')
 
@@ -59,9 +59,9 @@ def test_execution_tractogram_point_math_mean_4D_correlation(script_runner):
 
     ret = script_runner.run('scil_tractogram_dpp_math.py',
                             'correlation',
-                            'dps',
                             fodf_on_bundle,
                             'fodf_correlation_on_streamlines.trk',
+                            '--mode', 'dpp',
                             '--in_dpp_name', 'fodf',
                             '--out_name', 'fodf_correlation')
 

From efa733a4af7e48d458416ba31cb27ec34f2b787a Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 19 Feb 2024 11:53:17 -0500
Subject: [PATCH 91/97] added keep_all_dpp_dps option

---
 scripts/scil_tractogram_dpp_math.py | 46 +++++++++++++----------------
 1 file changed, 20 insertions(+), 26 deletions(-)

diff --git a/scripts/scil_tractogram_dpp_math.py b/scripts/scil_tractogram_dpp_math.py
index fe01a0380..5784e8e04 100755
--- a/scripts/scil_tractogram_dpp_math.py
+++ b/scripts/scil_tractogram_dpp_math.py
@@ -56,15 +56,15 @@ def _build_arg_parser():
                    help='The type of operation to be performed on the \n'
                         'streamlines. Must\nbe one of the following: \n'
                         '%(choices)s.')
+    p.add_argument('in_tractogram', metavar='INPUT_FILE',
+                   help='Input tractogram containing streamlines and \n'
+                        'metadata.')
     p.add_argument('--mode', required=True, choices=['dpp', 'dps'],
                    help='Set to dps if the operation is to be performed \n'
                    'across all dimensions resulting in a single value per \n'
                    'streamline. Set to dpp if the operation is to be \n'
                    'performed on each point separately resulting in a single \n'
                    'value per point.')
-    p.add_argument('in_tractogram', metavar='INPUT_FILE',
-                   help='Input tractogram containing streamlines and \n'
-                        'metadata.')
     p.add_argument('--in_dpp_name',  nargs='+', required=True,
                    help='Name or list of names of the data_per_point for \n'
                         'operation to be performed on. If more than one dpp \n'
@@ -78,15 +78,19 @@ def _build_arg_parser():
     p.add_argument('out_tractogram', metavar='OUTPUT_FILE',
                    help='The file where the remaining streamlines \n'
                         'are saved.')
-
     p.add_argument('--endpoints_only', action='store_true', default=False,
                    help='If set, will only perform operation on endpoints \n'
                    'If not set, will perform operation on all streamline \n'
                    'points.')
-    p.add_argument('--overwrite_data', action='store_true', default=False,
-                   help='If set, will overwrite the data_per_point or \n'
-                   'data_per_streamline in the output tractogram, otherwise \n'
-                   'previous data will be preserved in the output tractogram.')
+    p.add_argument('--keep_all_dpp_dps', action='store_true',
+                   help='If set, previous data_per_point will be preserved \n'
+                   'in the output tractogram. Else, only --out_dpp_name \n'
+                   'keys will be saved.')
+    p.add_argument('--overwrite_dpp_dps', action='store_true',
+                   help='If set, if --keep_all_dpp_dps is set and some \n'
+                   '--out_dpp_name keys already existed in your \n'
+                   ' data_per_point or data_per_streamline, allow \n'
+                   ' overwriting old data_per_point.')
 
     add_reference_arg(p)
     add_verbose_arg(p)
@@ -141,10 +145,10 @@ def main():
             logging.info('Correlation operation requires dps mode. Exiting.')
             return
 
-        if not args.overwrite_data:
+        if not args.overwrite_dpp_dps:
             if in_dpp_name in args.out_name:
                 logging.info('out_name {} already exists in input tractogram. '
-                             'Set overwrite_data or choose a different '
+                             'Set overwrite_dpp_dps or choose a different '
                              'out_name. Exiting.'.format(in_dpp_name))
                 return
 
@@ -178,25 +182,15 @@ def main():
                 args.operation, sft, in_dpp_name, args.endpoints_only)
             data_per_streamline[out_name] = new_data_per_streamline
 
-    if args.overwrite_data:
+    if args.keep_all_dpp_dps:
+        sft.data_per_streamline.update(data_per_streamline)
+        sft.data_per_point.update(data_per_point)
+
+        new_sft = sft
+    else:
         new_sft = sft.from_sft(sft.streamlines, sft,
                                data_per_point=data_per_point,
                                data_per_streamline=data_per_streamline)
-    else:
-        old_data_per_streamline = sft.data_per_streamline
-        old_data_per_point = sft.data_per_point
-
-        if data_per_point is not None:
-            for key, value in data_per_point.items():
-                old_data_per_point[key] = value
-
-        if data_per_streamline is not None:
-            for key, value in data_per_streamline.items():
-                old_data_per_streamline[key] = value
-
-        new_sft = sft.from_sft(sft.streamlines, sft,
-                               data_per_point=old_data_per_point,
-                               data_per_streamline=old_data_per_streamline)
 
     # Print DPP names
     logging.info('New data per point names:')

From f4b4e394fb8a317f8b4668e03e27077f16b5d6b1 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 19 Feb 2024 12:04:58 -0500
Subject: [PATCH 92/97] moved streamline ops to dps_and_dpp

---
 scilpy/tractograms/dps_and_dpp_management.py | 141 ++++++++++++++++++
 scilpy/tractograms/streamline_operations.py  | 143 +------------------
 scripts/scil_tractogram_dpp_math.py          |  27 ++--
 3 files changed, 160 insertions(+), 151 deletions(-)

diff --git a/scilpy/tractograms/dps_and_dpp_management.py b/scilpy/tractograms/dps_and_dpp_management.py
index 4fcdd8e21..1f85ef2dc 100644
--- a/scilpy/tractograms/dps_and_dpp_management.py
+++ b/scilpy/tractograms/dps_and_dpp_management.py
@@ -61,3 +61,144 @@ def project_map_to_streamlines(sft, map_volume, endpoints_only=False):
                            (len(thisstreamline_data), dimension)))
 
     return streamline_data
+
+
+def perform_streamline_operation_per_point(op_name, sft, dpp_name='metric',
+                                           endpoints_only=False):
+    """Peforms an operation per point for all streamlines.
+
+    Parameters
+    ----------
+    op_name: str
+        A callable that takes a list of streamline data per point (4D) and
+        returns a list of streamline data per point.
+    sft: StatefulTractogram
+        The streamlines used in the operation.
+    dpp_name: str
+        The name of the data per point to be used in the operation.
+    endpoints_only: bool
+        If True, will only perform operation on endpoints
+
+    Returns
+    -------
+    new_sft: StatefulTractogram
+        sft with data per streamline resulting from the operation.
+    """
+
+    # Performing operation
+    call_op = OPERATIONS[op_name]
+    if endpoints_only:
+        new_data_per_point = []
+        for s in sft.data_per_point[dpp_name]:
+            this_data_per_point = np.nan * np.ones((len(s), 1))
+            this_data_per_point[0] = call_op(s[0])
+            this_data_per_point[-1] = call_op(s[-1])
+            new_data_per_point.append(
+                np.reshape(this_data_per_point, (len(this_data_per_point), 1)))
+    else:
+        new_data_per_point = []
+        for s in sft.data_per_point[dpp_name]:
+            this_data_per_point = []
+            for p in s:
+                this_data_per_point.append(call_op(p))
+            new_data_per_point.append(
+                np.reshape(this_data_per_point, (len(this_data_per_point), 1)))
+
+    # Extracting streamlines
+    return new_data_per_point
+
+
+def perform_operation_per_streamline(op_name, sft, dpp_name='metric',
+                                     endpoints_only=False):
+    """Performs an operation across all data points for each streamline.
+
+    Parameters
+    ----------
+    op_name: str
+        A callable that takes a list of streamline data per streamline and
+        returns a list of data per streamline.
+    sft: StatefulTractogram
+        The streamlines used in the operation.
+    dpp_name: str
+        The name of the data per point to be used in the operation.
+    endpoints_only: bool
+        If True, will only perform operation on endpoints
+
+    Returns
+    -------
+    new_sft: StatefulTractogram
+        sft with data per streamline resulting from the operation.
+    """
+    # Performing operation
+    call_op = OPERATIONS[op_name]
+    if endpoints_only:
+        new_data_per_streamline = []
+        for s in sft.data_per_point[dpp_name]:
+            start = s[0]
+            end = s[-1]
+            concat = np.concatenate((start[:], end[:]))
+            new_data_per_streamline.append(call_op(concat))
+    else:
+        new_data_per_streamline = []
+        for s in sft.data_per_point[dpp_name]:
+            s_np = np.asarray(s)
+            new_data_per_streamline.append(call_op(s_np))
+
+    return new_data_per_streamline
+
+
+def perform_pairwise_streamline_operation_on_endpoints(op_name, sft,
+                                                       dpp_name='metric'):
+    """Peforms an operation across endpoints for each streamline.
+
+    Parameters
+    ----------
+    op_name: str
+        A callable that takes a list of streamline data per streamline and
+        returns a list of data per streamline.
+    sft: StatefulTractogram
+        The streamlines used in the operation.
+    dpp_name: str
+        The name of the data per point to be used in the operation.
+
+    Returns
+    -------
+    new_sft: StatefulTractogram
+        sft with data per streamline resulting from the operation.
+    """
+    # Performing operation
+    call_op = OPERATIONS[op_name]
+    new_data_per_streamline = []
+    for s in sft.data_per_point[dpp_name]:
+        new_data_per_streamline.append(call_op(s[0], s[-1])[0, 1])
+
+    return new_data_per_streamline
+
+
+def stream_mean(array):
+    return np.squeeze(np.mean(array, axis=0))
+
+
+def stream_sum(array):
+    return np.squeeze(np.sum(array, axis=0))
+
+
+def stream_min(array):
+    return np.squeeze(np.min(array, axis=0))
+
+
+def stream_max(array):
+    return np.squeeze(np.max(array, axis=0))
+
+
+def stream_correlation(array1, array2):
+    return np.corrcoef(array1, array2)
+
+
+OPERATIONS = {
+    'mean': stream_mean,
+    'sum': stream_sum,
+    'min': stream_min,
+    'max': stream_max,
+    'correlation': stream_correlation,
+}
diff --git a/scilpy/tractograms/streamline_operations.py b/scilpy/tractograms/streamline_operations.py
index 3a98316e0..f51d56256 100644
--- a/scilpy/tractograms/streamline_operations.py
+++ b/scilpy/tractograms/streamline_operations.py
@@ -387,145 +387,4 @@ def smooth_line_spline(streamline, smoothing_parameter, nb_ctrl_points):
     smoothed_streamline[0] = streamline[0]
     smoothed_streamline[-1] = streamline[-1]
 
-    return smoothed_streamline
-
-
-def perform_streamline_operation_per_point(op_name, sft, dpp_name='metric',
-                                           endpoints_only=False):
-    """Peforms an operation per point for all streamlines.
-
-    Parameters
-    ----------
-    op_name: str
-        A callable that takes a list of streamline data per point (4D) and
-        returns a list of streamline data per point.
-    sft: StatefulTractogram
-        The streamlines used in the operation.
-    dpp_name: str
-        The name of the data per point to be used in the operation.
-    endpoints_only: bool
-        If True, will only perform operation on endpoints
-
-    Returns
-    -------
-    new_sft: StatefulTractogram
-        sft with data per streamline resulting from the operation.
-    """
-
-    # Performing operation
-    call_op = OPERATIONS[op_name]
-    if endpoints_only:
-        new_data_per_point = []
-        for s in sft.data_per_point[dpp_name]:
-            this_data_per_point = np.nan * np.ones((len(s), 1))
-            this_data_per_point[0] = call_op(s[0])
-            this_data_per_point[-1] = call_op(s[-1])
-            new_data_per_point.append(
-                np.reshape(this_data_per_point, (len(this_data_per_point), 1)))
-    else:
-        new_data_per_point = []
-        for s in sft.data_per_point[dpp_name]:
-            this_data_per_point = []
-            for p in s:
-                this_data_per_point.append(call_op(p))
-            new_data_per_point.append(
-                np.reshape(this_data_per_point, (len(this_data_per_point), 1)))
-
-    # Extracting streamlines
-    return new_data_per_point
-
-
-def perform_operation_per_streamline(op_name, sft, dpp_name='metric',
-                                     endpoints_only=False):
-    """Performs an operation across all data points for each streamline.
-
-    Parameters
-    ----------
-    op_name: str
-        A callable that takes a list of streamline data per streamline and
-        returns a list of data per streamline.
-    sft: StatefulTractogram
-        The streamlines used in the operation.
-    dpp_name: str
-        The name of the data per point to be used in the operation.
-    endpoints_only: bool
-        If True, will only perform operation on endpoints
-
-    Returns
-    -------
-    new_sft: StatefulTractogram
-        sft with data per streamline resulting from the operation.
-    """
-    # Performing operation
-    call_op = OPERATIONS[op_name]
-    if endpoints_only:
-        new_data_per_streamline = []
-        for s in sft.data_per_point[dpp_name]:
-            start = s[0]
-            end = s[-1]
-            concat = np.concatenate((start[:], end[:]))
-            new_data_per_streamline.append(call_op(concat))
-    else:
-        new_data_per_streamline = []
-        for s in sft.data_per_point[dpp_name]:
-            s_np = np.asarray(s)
-            new_data_per_streamline.append(call_op(s_np))
-
-    return new_data_per_streamline
-
-
-def perform_pairwise_streamline_operation_on_endpoints(op_name, sft,
-                                                       dpp_name='metric'):
-    """Peforms an operation across endpoints for each streamline.
-
-    Parameters
-    ----------
-    op_name: str
-        A callable that takes a list of streamline data per streamline and
-        returns a list of data per streamline.
-    sft: StatefulTractogram
-        The streamlines used in the operation.
-    dpp_name: str
-        The name of the data per point to be used in the operation.
-
-    Returns
-    -------
-    new_sft: StatefulTractogram
-        sft with data per streamline resulting from the operation.
-    """
-    # Performing operation
-    call_op = OPERATIONS[op_name]
-    new_data_per_streamline = []
-    for s in sft.data_per_point[dpp_name]:
-        new_data_per_streamline.append(call_op(s[0], s[-1])[0, 1])
-
-    return new_data_per_streamline
-
-
-def stream_mean(array):
-    return np.squeeze(np.mean(array, axis=0))
-
-
-def stream_sum(array):
-    return np.squeeze(np.sum(array, axis=0))
-
-
-def stream_min(array):
-    return np.squeeze(np.min(array, axis=0))
-
-
-def stream_max(array):
-    return np.squeeze(np.max(array, axis=0))
-
-
-def stream_correlation(array1, array2):
-    return np.corrcoef(array1, array2)
-
-
-OPERATIONS = {
-    'mean': stream_mean,
-    'sum': stream_sum,
-    'min': stream_min,
-    'max': stream_max,
-    'correlation': stream_correlation,
-}
+    return smoothed_streamline
\ No newline at end of file
diff --git a/scripts/scil_tractogram_dpp_math.py b/scripts/scil_tractogram_dpp_math.py
index 5784e8e04..6d4bb8baf 100755
--- a/scripts/scil_tractogram_dpp_math.py
+++ b/scripts/scil_tractogram_dpp_math.py
@@ -39,12 +39,11 @@
                              add_verbose_arg,
                              assert_inputs_exist,
                              assert_outputs_exist)
-from scilpy.tractograms.streamline_operations import (
+from scilpy.tractograms.dps_and_dpp_management import (
         perform_pairwise_streamline_operation_on_endpoints,
         perform_streamline_operation_per_point,
         perform_operation_per_streamline)
 
-
 def _build_arg_parser():
     p = argparse.ArgumentParser(
         formatter_class=argparse.RawTextHelpFormatter,
@@ -134,9 +133,15 @@ def main():
                          .format(in_dpp_name))
             return
 
+        if args.dpp_or_dps == 'dpp' and (len(data_shape) == 1 or
+                                         data_shape[1] == 1):
+            logging.warning('dpp from key {} is a single number per point. '
+                            'Performing a dpp-mode operation on this data '
+                            'will not do anything. Continuing.')
+
         # Check if first data_per_point is multivalued
         data_shape = sft.data_per_point[in_dpp_name][0].shape
-        if args.operation == 'correlation' and len(data_shape) == 1:
+        if args.operation == 'correlation' and len(data_shape) == 2 and data_shape[1] > 1:
             logging.info('Correlation operation requires multivalued data per '
                          'point. Exiting.')
             return
@@ -193,14 +198,18 @@ def main():
                                data_per_streamline=data_per_streamline)
 
     # Print DPP names
-    logging.info('New data per point names:')
-    for key in new_sft.data_per_point.keys():
-        logging.info(key)
+    if data_per_point not in [None, {}]:
+        print("New data_per_point keys are: ")
+        for key in args.out_name:
+            print("  - {} with shape per point {}"
+                .format(key, new_sft.data_per_point[key][0].shape[1:]))
 
     # Print DPS names
-    logging.info('New data per streamline names:')
-    for key in new_sft.data_per_streamline.keys():
-        logging.info(key)
+    if data_per_streamline not in [None, {}]:
+        print("New data_per_streamline keys are: ")
+        for key in args.out_name:
+            print("  - {} with shape per streamline {}"
+                .format(key, new_sft.data_per_streamline[key].shape[1:]))
 
     # Save the new streamlines (and metadata)
     logging.info('Saving {} streamlines to {}.'.format(len(new_sft),

From e0e70a3e8c94043a784e330ace05f1a741119aca Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 19 Feb 2024 12:15:36 -0500
Subject: [PATCH 93/97] blank tests to dps_dpp module

---
 .../tests/test_dps_and_dpp_management.py          | 15 +++++++++++++++
 .../tests/test_streamline_operations.py           | 15 ---------------
 2 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/scilpy/tractograms/tests/test_dps_and_dpp_management.py b/scilpy/tractograms/tests/test_dps_and_dpp_management.py
index fb93d736a..1fc2a7e88 100644
--- a/scilpy/tractograms/tests/test_dps_and_dpp_management.py
+++ b/scilpy/tractograms/tests/test_dps_and_dpp_management.py
@@ -1,3 +1,18 @@
 def test_project_map_to_streamlines():
     # toDo
     pass
+
+
+def test_perform_streamline_operation_per_point():
+    # toDo
+    pass
+
+
+def test_perform_operation_per_streamline():
+    # toDo
+    pass
+
+
+def test_perform_streamline_operation_on_endpoints():
+    # toDo
+    pass
diff --git a/scilpy/tractograms/tests/test_streamline_operations.py b/scilpy/tractograms/tests/test_streamline_operations.py
index f8e0d4e8a..faeb4e57c 100644
--- a/scilpy/tractograms/tests/test_streamline_operations.py
+++ b/scilpy/tractograms/tests/test_streamline_operations.py
@@ -367,18 +367,3 @@ def test_smooth_line_spline():
     dist_2 = np.linalg.norm(noisy_streamline - smoothed_streamline)
 
     assert dist_1 < dist_2
-
-
-def test_perform_streamline_operation_per_point():
-    # toDo
-    pass
-
-
-def test_perform_operation_per_streamline():
-    # toDo
-    pass
-
-
-def test_perform_streamline_operation_on_endpoints():
-    # toDo
-    pass

From 6d752e5640dfc0b20708b0a95a2756f1f0c762ee Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 19 Feb 2024 12:23:54 -0500
Subject: [PATCH 94/97] pep8

---
 scilpy/tractograms/streamline_operations.py      |  2 +-
 scripts/scil_tractogram_dpp_math.py              | 16 +++++++++-------
 ...scil_tractogram_project_map_to_streamlines.py | 10 +++++-----
 3 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/scilpy/tractograms/streamline_operations.py b/scilpy/tractograms/streamline_operations.py
index f51d56256..7df3a396c 100644
--- a/scilpy/tractograms/streamline_operations.py
+++ b/scilpy/tractograms/streamline_operations.py
@@ -387,4 +387,4 @@ def smooth_line_spline(streamline, smoothing_parameter, nb_ctrl_points):
     smoothed_streamline[0] = streamline[0]
     smoothed_streamline[-1] = streamline[-1]
 
-    return smoothed_streamline
\ No newline at end of file
+    return smoothed_streamline
diff --git a/scripts/scil_tractogram_dpp_math.py b/scripts/scil_tractogram_dpp_math.py
index 6d4bb8baf..f391976ef 100755
--- a/scripts/scil_tractogram_dpp_math.py
+++ b/scripts/scil_tractogram_dpp_math.py
@@ -10,8 +10,8 @@
    - In dps mode, the operation is performed on dpp across the dimension of
    the streamlines resulting in a single value (or array in the 4D case)
    per streamline, stored as dps.
-   - In dpp mode, the operation is performed on each point separately, resulting in
-   a new dpp.
+   - In dpp mode, the operation is performed on each point separately,
+   resulting in a new dpp.
 
 If endpoints_only and dpp mode is set the operation will only
 be calculated at the streamline endpoints the rest of the
@@ -44,6 +44,7 @@
         perform_streamline_operation_per_point,
         perform_operation_per_streamline)
 
+
 def _build_arg_parser():
     p = argparse.ArgumentParser(
         formatter_class=argparse.RawTextHelpFormatter,
@@ -62,8 +63,8 @@ def _build_arg_parser():
                    help='Set to dps if the operation is to be performed \n'
                    'across all dimensions resulting in a single value per \n'
                    'streamline. Set to dpp if the operation is to be \n'
-                   'performed on each point separately resulting in a single \n'
-                   'value per point.')
+                   'performed on each point separately resulting in a \n'
+                   'single value per point.')
     p.add_argument('--in_dpp_name',  nargs='+', required=True,
                    help='Name or list of names of the data_per_point for \n'
                         'operation to be performed on. If more than one dpp \n'
@@ -141,7 +142,8 @@ def main():
 
         # Check if first data_per_point is multivalued
         data_shape = sft.data_per_point[in_dpp_name][0].shape
-        if args.operation == 'correlation' and len(data_shape) == 2 and data_shape[1] > 1:
+        if args.operation == 'correlation' and len(data_shape) == 2 \
+                                                and data_shape[1] > 1:
             logging.info('Correlation operation requires multivalued data per '
                          'point. Exiting.')
             return
@@ -202,14 +204,14 @@ def main():
         print("New data_per_point keys are: ")
         for key in args.out_name:
             print("  - {} with shape per point {}"
-                .format(key, new_sft.data_per_point[key][0].shape[1:]))
+                  .format(key, new_sft.data_per_point[key][0].shape[1:]))
 
     # Print DPS names
     if data_per_streamline not in [None, {}]:
         print("New data_per_streamline keys are: ")
         for key in args.out_name:
             print("  - {} with shape per streamline {}"
-                .format(key, new_sft.data_per_streamline[key].shape[1:]))
+                  .format(key, new_sft.data_per_streamline[key].shape[1:]))
 
     # Save the new streamlines (and metadata)
     logging.info('Saving {} streamlines to {}.'.format(len(new_sft),
diff --git a/scripts/scil_tractogram_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
index e7578a80b..027515781 100755
--- a/scripts/scil_tractogram_project_map_to_streamlines.py
+++ b/scripts/scil_tractogram_project_map_to_streamlines.py
@@ -55,13 +55,13 @@ def _build_arg_parser():
                    'the map onto all points of the streamlines.')
 
     p.add_argument('--keep_all_dpp', action='store_true',
-                   help='If set, previous data_per_point will be preserved '
-                   'in the output tractogram. Else, only --out_dpp_name '
+                   help='If set, previous data_per_point will be preserved \n'
+                   'in the output tractogram. Else, only --out_dpp_name \n'
                    'keys will be saved.')
     p.add_argument('--overwrite_dpp', action='store_true',
-                   help='If set, if --keep_all_dpp is set and some --out_dpp_name '
-                   'keys already existed in your data_per_point, allow overwriting '
-                   'old data_per_point.')
+                   help='If set, if --keep_all_dpp is set and some \n'
+                   '--out_dpp_name keys already existed in your \n'
+                   'data_per_point, allow overwriting old data_per_point.')
 
     add_reference_arg(p)
     add_overwrite_arg(p)

From a21aa16f221ee12576bd9c7c02367531cd2eaae1 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 19 Feb 2024 12:47:02 -0500
Subject: [PATCH 95/97] 4D data stored as shape (#,) fixed checks

---
 scripts/scil_tractogram_dpp_math.py | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/scripts/scil_tractogram_dpp_math.py b/scripts/scil_tractogram_dpp_math.py
index f391976ef..bdb54faf2 100755
--- a/scripts/scil_tractogram_dpp_math.py
+++ b/scripts/scil_tractogram_dpp_math.py
@@ -40,9 +40,9 @@
                              assert_inputs_exist,
                              assert_outputs_exist)
 from scilpy.tractograms.dps_and_dpp_management import (
-        perform_pairwise_streamline_operation_on_endpoints,
-        perform_streamline_operation_per_point,
-        perform_operation_per_streamline)
+    perform_pairwise_streamline_operation_on_endpoints,
+    perform_streamline_operation_per_point,
+    perform_operation_per_streamline)
 
 
 def _build_arg_parser():
@@ -134,16 +134,15 @@ def main():
                          .format(in_dpp_name))
             return
 
-        if args.dpp_or_dps == 'dpp' and (len(data_shape) == 1 or
-                                         data_shape[1] == 1):
+        # warning if dpp mode and data in single number per point
+        data_shape = sft.data_per_point[in_dpp_name][0].shape
+        if args.mode == 'dpp' and data_shape[0] == 1:
             logging.warning('dpp from key {} is a single number per point. '
                             'Performing a dpp-mode operation on this data '
                             'will not do anything. Continuing.')
 
         # Check if first data_per_point is multivalued
-        data_shape = sft.data_per_point[in_dpp_name][0].shape
-        if args.operation == 'correlation' and len(data_shape) == 2 \
-                                                and data_shape[1] > 1:
+        if args.operation == 'correlation' and data_shape > 1:
             logging.info('Correlation operation requires multivalued data per '
                          'point. Exiting.')
             return

From 8db77a91ecb8fe5d7913fecb2562fcc1341aede1 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 19 Feb 2024 12:47:48 -0500
Subject: [PATCH 96/97] fixed dimension on tuple

---
 scripts/scil_tractogram_dpp_math.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/scil_tractogram_dpp_math.py b/scripts/scil_tractogram_dpp_math.py
index bdb54faf2..80fbd091f 100755
--- a/scripts/scil_tractogram_dpp_math.py
+++ b/scripts/scil_tractogram_dpp_math.py
@@ -142,7 +142,7 @@ def main():
                             'will not do anything. Continuing.')
 
         # Check if first data_per_point is multivalued
-        if args.operation == 'correlation' and data_shape > 1:
+        if args.operation == 'correlation' and data_shape[0] > 1:
             logging.info('Correlation operation requires multivalued data per '
                          'point. Exiting.')
             return

From 47f287bd224dbebf11e33ac063425d3772d0f796 Mon Sep 17 00:00:00 2001
From: grahamlittlephd <grahamlittlephd@gmail.com>
Date: Mon, 19 Feb 2024 12:57:57 -0500
Subject: [PATCH 97/97] updated dimension on data_shape

---
 scripts/scil_tractogram_dpp_math.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/scil_tractogram_dpp_math.py b/scripts/scil_tractogram_dpp_math.py
index 80fbd091f..bedaace47 100755
--- a/scripts/scil_tractogram_dpp_math.py
+++ b/scripts/scil_tractogram_dpp_math.py
@@ -142,7 +142,7 @@ def main():
                             'will not do anything. Continuing.')
 
         # Check if first data_per_point is multivalued
-        if args.operation == 'correlation' and data_shape[0] > 1:
+        if args.operation == 'correlation' and data_shape[0] == 1:
             logging.info('Correlation operation requires multivalued data per '
                          'point. Exiting.')
             return