From 87201dbbd0765198e6a8734d5abb6ad1b14997c6 Mon Sep 17 00:00:00 2001
From: VincentBeaud <vincent.beaudoin@icloud.com>
Date: Tue, 26 Nov 2024 10:14:00 -0500
Subject: [PATCH 01/10] Generalize data_per_streamline operations

---
 scripts/scil_tractogram_add_dps.py  |  83 ------------------
 scripts/scil_tractogram_dps_math.py | 125 ++++++++++++++++++++++++++++
 2 files changed, 125 insertions(+), 83 deletions(-)
 delete mode 100755 scripts/scil_tractogram_add_dps.py
 create mode 100755 scripts/scil_tractogram_dps_math.py

diff --git a/scripts/scil_tractogram_add_dps.py b/scripts/scil_tractogram_add_dps.py
deleted file mode 100755
index b688efe0b..000000000
--- a/scripts/scil_tractogram_add_dps.py
+++ /dev/null
@@ -1,83 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-""" Add information to each streamline from a file. Can be for example
-SIFT2 weights, processing information, bundle IDs, etc.
-
-Output must be a .trk otherwise the data will be lost.
-"""
-
-import argparse
-import logging
-
-from dipy.io.streamline import save_tractogram
-import numpy as np
-
-from scilpy.io.streamlines import load_tractogram_with_reference
-from scilpy.io.utils import (add_overwrite_arg,
-                             add_reference_arg,
-                             add_verbose_arg,
-                             assert_inputs_exist,
-                             assert_outputs_exist,
-                             check_tract_trk,
-                             load_matrix_in_any_format)
-
-
-def _build_arg_parser():
-
-    p = argparse.ArgumentParser(
-        description=__doc__,
-        formatter_class=argparse.RawTextHelpFormatter)
-
-    p.add_argument('in_tractogram',
-                   help='Input tractogram (.trk or .tck).')
-    p.add_argument('in_dps_file',
-                   help='File containing the data to add to streamlines.')
-    p.add_argument('dps_key',
-                   help='Where to store the data in the tractogram.')
-    p.add_argument('out_tractogram',
-                   help='Output tractogram (.trk).')
-
-    add_reference_arg(p)
-    add_verbose_arg(p)
-    add_overwrite_arg(p)
-
-    return p
-
-
-def main():
-    parser = _build_arg_parser()
-    args = parser.parse_args()
-    logging.getLogger().setLevel(logging.getLevelName(args.verbose))
-
-    # I/O assertions
-    assert_inputs_exist(parser, [args.in_tractogram, args.in_dps_file],
-                        args.reference)
-    assert_outputs_exist(parser, args, args.out_tractogram)
-    check_tract_trk(parser, args.out_tractogram)
-
-    # Load tractogram
-    sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
-
-    # Make sure the user is not unwillingly overwritting dps
-    if (args.dps_key in sft.get_data_per_streamline_keys() and
-       not args.overwrite):
-        parser.error('"{}" already in data per streamline. Use -f to force '
-                     'overwriting.'.format(args.dps_key))
-
-    # Load data and remove extraneous dimensions
-    data = np.squeeze(load_matrix_in_any_format(args.in_dps_file))
-
-    # Quick check as the built-in error from sft is not too explicit
-    if len(sft) != data.shape[0]:
-        raise ValueError('Data must have as many entries ({}) as there are'
-                         ' streamlines ({}).'.format(data.shape[0], len(sft)))
-    # Add data to tractogram
-    sft.data_per_streamline[args.dps_key] = data
-
-    # Save the new sft
-    save_tractogram(sft, args.out_tractogram)
-
-
-if __name__ == '__main__':
-    main()
diff --git a/scripts/scil_tractogram_dps_math.py b/scripts/scil_tractogram_dps_math.py
new file mode 100755
index 000000000..d284b9ec8
--- /dev/null
+++ b/scripts/scil_tractogram_dps_math.py
@@ -0,0 +1,125 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+Add, extract or delete information to each streamline from a tractogram
+file. Can be for example SIFT2 weights, processing information, bundle IDs,
+etc.
+
+Input and output tractograms must always be .trk to simplify filetype checks
+for each operation.
+"""
+
+import os
+import argparse
+import logging
+
+from dipy.io.streamline import save_tractogram, load_tractogram
+import numpy as np
+
+from scilpy.io.utils import (add_overwrite_arg,
+                             add_verbose_arg,
+                             assert_inputs_exist,
+                             assert_outputs_exist,
+                             check_tract_trk,
+                             load_matrix_in_any_format,
+                             save_matrix_in_any_format)
+
+
+def _build_arg_parser():
+
+    p = argparse.ArgumentParser(
+        description=__doc__,
+        formatter_class=argparse.RawTextHelpFormatter)
+
+    p.add_argument('in_tractogram',
+                   help='Input tractogram (.trk).')
+    p.add_argument('operation', metavar='OPERATION',
+                   choices=['add', 'delete', 'export'],
+                   help='The type of operation to be performed on the\n'
+                        'tractogram\'s data_per_streamline. Must be one of\n'
+                        'the following: [%(choices)s]. The arguments\n'
+                        'required for each operation are specified under\n'
+                        'each group below.')
+
+    add_args = p.add_argument_group('Add operation',
+                                    'Requires the out_tractogram argument.')
+    add_args.add_argument('--add_dps_file',
+                          help='File containing the data to add to\n'
+                               'streamlines.')
+    add_args.add_argument('--add_dps_key', type=str,
+                          help='Where to store the data in the tractogram.')
+
+    delete_args = p.add_argument_group('Delete operation',
+                                       'Requires the out_tractogram argument.')
+    delete_args.add_argument('--delete_dps_key', type=str,
+                             help='Where to find the data to be deleted, in\n'
+                                  'the tractogram.')
+
+    p.add_argument('--out_tractogram',
+                   help='Output tractogram (.trk). Required for any mutation.')
+
+    export_args = p.add_argument_group('Export operation')
+    export_args.add_argument('--export_dps_key', type=str,
+                             help='Where to find the data to be exported,\n'
+                                  'in the tractogram.')
+    export_args.add_argument('--export_dps_file',
+                             help='File in which the extracted data will be\n'
+                                  'saved.')
+
+    add_verbose_arg(p)
+    add_overwrite_arg(p)
+
+    return p
+
+
+def main():
+    parser = _build_arg_parser()
+    args = parser.parse_args()
+    logging.getLogger().setLevel(logging.getLevelName(args.verbose))
+
+    check_tract_trk(parser, args.in_tractogram)
+    if args.out_tractogram:
+        check_tract_trk(parser, args.out_tractogram)
+
+    # I/O assertions
+    assert_inputs_exist(parser, args.in_tractogram, args.add_dps_file)
+    assert_outputs_exist(parser, args, [], optional=[args.export_dps_file,
+                                                     args.out_tractogram])
+
+    sft = load_tractogram(args.in_tractogram, 'same')
+
+    if args.operation == 'add':
+        # Make sure the user is not unwillingly overwritting dps
+        if (args.add_dps_key in sft.get_data_per_streamline_keys() and
+                not args.overwrite):
+            parser.error('"{}" already in data per streamline. Use -f to force'
+                         ' overwriting.'.format(args.add_dps_key))
+
+        # Load data and remove extraneous dimensions
+        data = np.squeeze(load_matrix_in_any_format(args.add_dps_file))
+
+        # Quick check as the built-in error from sft is not too explicit
+        if len(sft) != data.shape[0]:
+            raise ValueError('Data must have as many entries ({}) as there are'
+                             ' streamlines ({}).'.format(data.shape[0],
+                                                         len(sft)))
+
+        sft.data_per_streamline[args.add_dps_key] = data
+
+        save_tractogram(sft, args.out_tractogram)
+
+    if args.operation == 'delete':
+        del sft.data_per_streamline[args.delete_dps_key]
+
+        save_tractogram(sft, args.out_tractogram)
+
+    if args.operation == 'export':
+        # Extract data and reshape
+        data = np.squeeze(sft.data_per_streamline[args.export_dps_key])
+
+        save_matrix_in_any_format(args.export_dps_file, data)
+
+
+if __name__ == '__main__':
+    main()

From bb96b054591fa555c15948dbff10de44175ba19c Mon Sep 17 00:00:00 2001
From: VincentBeaud <vincent.beaudoin@icloud.com>
Date: Tue, 26 Nov 2024 14:25:51 -0500
Subject: [PATCH 02/10] tests for scil_tractogram_dps_math.py

---
 scripts/scil_tractogram_dps_math.py       |   6 +-
 scripts/tests/test_tractogram_add_dps.py  |  77 -----------
 scripts/tests/test_tractogram_dps_math.py | 151 ++++++++++++++++++++++
 3 files changed, 156 insertions(+), 78 deletions(-)
 delete mode 100644 scripts/tests/test_tractogram_add_dps.py
 create mode 100644 scripts/tests/test_tractogram_dps_math.py

diff --git a/scripts/scil_tractogram_dps_math.py b/scripts/scil_tractogram_dps_math.py
index d284b9ec8..187532d20 100755
--- a/scripts/scil_tractogram_dps_math.py
+++ b/scripts/scil_tractogram_dps_math.py
@@ -116,8 +116,12 @@ def main():
 
     if args.operation == 'export':
         # Extract data and reshape
-        data = np.squeeze(sft.data_per_streamline[args.export_dps_key])
+        if not args.export_dps_key in sft.data_per_streamline.keys():
+            raise ValueError('Data does not have any data_per_streamline'
+                             ' entry stored at this key: {}'
+                                .format(args.export_dps_key))
 
+        data = np.squeeze(sft.data_per_streamline[args.export_dps_key])
         save_matrix_in_any_format(args.export_dps_file, data)
 
 
diff --git a/scripts/tests/test_tractogram_add_dps.py b/scripts/tests/test_tractogram_add_dps.py
deleted file mode 100644
index b5e7f05d2..000000000
--- a/scripts/tests/test_tractogram_add_dps.py
+++ /dev/null
@@ -1,77 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-import numpy as np
-import os
-import tempfile
-
-from dipy.io.streamline import load_tractogram
-
-from scilpy import SCILPY_HOME
-from scilpy.io.fetcher import fetch_data, get_testing_files_dict
-
-# If they already exist, this only takes 5 seconds (check md5sum)
-fetch_data(get_testing_files_dict(), keys=['filtering.zip'])
-tmp_dir = tempfile.TemporaryDirectory()
-
-
-def test_help_option(script_runner):
-    ret = script_runner.run('scil_tractogram_add_dps.py',
-                            '--help')
-    assert ret.success
-
-
-def test_execution_add_dps(script_runner, monkeypatch):
-    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
-    in_bundle = os.path.join(SCILPY_HOME, 'filtering',
-                             'bundle_4.trk')
-    sft = load_tractogram(in_bundle, 'same')
-    filename = 'vals.npy'
-    outname = 'out.trk'
-    np.save(filename, np.arange(len(sft)))
-    ret = script_runner.run('scil_tractogram_add_dps.py',
-                            in_bundle, filename, 'key', outname, '-f')
-    assert ret.success
-
-
-def test_execution_add_dps_missing_vals(script_runner, monkeypatch):
-    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
-    in_bundle = os.path.join(SCILPY_HOME, 'filtering',
-                             'bundle_4.trk')
-    sft = load_tractogram(in_bundle, 'same')
-    filename = 'vals.npy'
-    outname = 'out.trk'
-    np.save(filename, np.arange(len(sft) - 10))
-    ret = script_runner.run('scil_tractogram_add_dps.py',
-                            in_bundle, filename, 'key', outname, '-f')
-    assert ret.stderr
-
-
-def test_execution_add_dps_existing_key(script_runner, monkeypatch):
-    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
-    in_bundle = os.path.join(SCILPY_HOME, 'filtering',
-                             'bundle_4.trk')
-    sft = load_tractogram(in_bundle, 'same')
-    filename = 'vals.npy'
-    outname = 'out.trk'
-    outname2 = 'out_2.trk'
-    np.save(filename, np.arange(len(sft)))
-    ret = script_runner.run('scil_tractogram_add_dps.py',
-                            in_bundle, filename, 'key', outname, '-f')
-    assert ret.success
-    ret = script_runner.run('scil_tractogram_add_dps.py',
-                            outname, filename, 'key', outname2)
-    assert not ret.success
-
-
-def test_execution_add_dps_tck(script_runner, monkeypatch):
-    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
-    in_bundle = os.path.join(SCILPY_HOME, 'filtering',
-                             'bundle_4.trk')
-    sft = load_tractogram(in_bundle, 'same')
-    filename = 'vals.npy'
-    outname = 'out.tck'
-    np.save(filename, np.arange(len(sft)))
-    ret = script_runner.run('scil_tractogram_add_dps.py',
-                            in_bundle, filename, 'key', outname, '-f')
-    assert not ret.success
diff --git a/scripts/tests/test_tractogram_dps_math.py b/scripts/tests/test_tractogram_dps_math.py
new file mode 100644
index 000000000..531fb8459
--- /dev/null
+++ b/scripts/tests/test_tractogram_dps_math.py
@@ -0,0 +1,151 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import numpy as np
+import os
+import tempfile
+
+from dipy.io.streamline import load_tractogram, save_tractogram
+
+from scilpy import SCILPY_HOME
+from scilpy.io.fetcher import fetch_data, get_testing_files_dict
+
+# If they already exist, this only takes 5 seconds (check md5sum)
+fetch_data(get_testing_files_dict(), keys=['filtering.zip'])
+tmp_dir = tempfile.TemporaryDirectory()
+
+
+def test_help_option(script_runner):
+    ret = script_runner.run('scil_tractogram_dps_math.py',
+                            '--help')
+    assert ret.success
+
+
+def test_execution_dps_math_add(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_bundle = os.path.join(SCILPY_HOME, 'filtering',
+                             'bundle_4.trk')
+    sft = load_tractogram(in_bundle, 'same')
+    filename = 'vals.npy'
+    outname = 'out.trk'
+    np.save(filename, np.arange(len(sft)))
+    ret = script_runner.run('scil_tractogram_dps_math.py', in_bundle, 'add',
+                            '--add_dps_file', filename,
+                            '--add_dps_key', 'key',
+                            '--out_tractogram', outname,
+                            '-f')
+    assert ret.success
+
+
+def test_execution_dps_math_add_with_missing_vals(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_bundle = os.path.join(SCILPY_HOME, 'filtering',
+                             'bundle_4.trk')
+    sft = load_tractogram(in_bundle, 'same')
+    filename = 'vals.npy'
+    outname = 'out.trk'
+    np.save(filename, np.arange(len(sft) - 10))
+    ret = script_runner.run('scil_tractogram_dps_math.py', in_bundle, 'add',
+                            '--add_dps_file', filename,
+                            '--add_dps_key', 'key',
+                            '--out_tractogram', outname,
+                            '-f')
+    assert ret.stderr
+
+
+def test_execution_dps_math_add_with_existing_key(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_bundle = os.path.join(SCILPY_HOME, 'filtering',
+                             'bundle_4.trk')
+    sft = load_tractogram(in_bundle, 'same')
+    filename = 'vals.npy'
+    outname = 'out.trk'
+    outname2 = 'out_2.trk'
+    np.save(filename, np.arange(len(sft)))
+    ret = script_runner.run('scil_tractogram_dps_math.py', in_bundle, 'add',
+                            '--add_dps_file', filename,
+                            '--add_dps_key', 'key',
+                            '--out_tractogram', outname,
+                            '-f')
+    assert ret.success
+    ret = script_runner.run('scil_tractogram_dps_math.py', outname, 'add',
+                            '--add_dps_file', filename,
+                            '--add_dps_key', 'key',
+                            '--out_tractogram', outname2,)
+    assert not ret.success
+
+
+def test_execution_dps_math_tck(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_bundle = os.path.join(SCILPY_HOME, 'filtering',
+                             'bundle_4.trk')
+    sft = load_tractogram(in_bundle, 'same')
+    filename = 'vals.npy'
+    outname = 'out.tck'
+    np.save(filename, np.arange(len(sft)))
+    ret = script_runner.run('scil_tractogram_dps_math.py', in_bundle, 'add',
+                            '--add_dps_file', filename,
+                            '--add_dps_key', 'key',
+                            '--out_tractogram', outname,
+                            '-f')
+    assert not ret.success
+
+
+def test_execution_dps_math_delete(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_bundle_no_key = os.path.join(SCILPY_HOME, 'filtering',
+                                    'bundle_4.trk')
+    in_bundle = 'bundle_4.trk'
+    sft = load_tractogram(in_bundle_no_key, 'same')
+    sft.data_per_streamline = {
+        "key": [0] * len(sft)
+    }
+    save_tractogram(sft, in_bundle)
+    outname = 'out.trk'
+    ret = script_runner.run('scil_tractogram_dps_math.py', in_bundle, 'delete',
+                            '--delete_dps_key', 'key',
+                            '--out_tractogram', outname,
+                            '-f')
+    assert ret.success
+
+
+def test_execution_dps_math_delete_no_key(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_bundle = os.path.join(SCILPY_HOME, 'filtering',
+                             'bundle_4.trk')
+    outname = 'out.trk'
+    ret = script_runner.run('scil_tractogram_dps_math.py', in_bundle, 'delete',
+                            '--delete_dps_key', 'key',
+                            '--out_tractogram', outname,
+                            '-f')
+    assert not ret.success
+
+
+def test_execution_dps_math_export(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_bundle_no_key = os.path.join(SCILPY_HOME, 'filtering',
+                                    'bundle_4.trk')
+    in_bundle = 'bundle_4.trk'
+    sft = load_tractogram(in_bundle_no_key, 'same')
+    sft.data_per_streamline = {
+        "key": [0] * len(sft)
+    }
+    save_tractogram(sft, in_bundle)
+    filename = 'out.txt'
+    ret = script_runner.run('scil_tractogram_dps_math.py', in_bundle, 'export',
+                            '--export_dps_key', 'key',
+                            '--export_dps_file', filename,
+                            '-f')
+    assert ret.success
+
+
+def test_execution_dps_math_export_no_key(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_bundle = os.path.join(SCILPY_HOME, 'filtering',
+                             'bundle_4.trk')
+    filename = 'out.txt'
+    ret = script_runner.run('scil_tractogram_dps_math.py', in_bundle, 'export',
+                            '--export_dps_key', 'key',
+                            '--export_dps_file', filename,
+                            '-f')
+    assert not ret.success

From 3883e1daec16e6698edaef3c4000872ded642185 Mon Sep 17 00:00:00 2001
From: VincentBeaud <vincent.beaudoin@icloud.com>
Date: Mon, 2 Dec 2024 12:27:02 -0500
Subject: [PATCH 03/10] Pep8 fix

---
 scripts/scil_tractogram_dps_math.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/scripts/scil_tractogram_dps_math.py b/scripts/scil_tractogram_dps_math.py
index 187532d20..3cd142461 100755
--- a/scripts/scil_tractogram_dps_math.py
+++ b/scripts/scil_tractogram_dps_math.py
@@ -4,7 +4,7 @@
 """
 Add, extract or delete information to each streamline from a tractogram
 file. Can be for example SIFT2 weights, processing information, bundle IDs,
-etc.
+tracking seeds, etc.
 
 Input and output tractograms must always be .trk to simplify filetype checks
 for each operation.
@@ -42,11 +42,14 @@ def _build_arg_parser():
                         'required for each operation are specified under\n'
                         'each group below.')
 
+    p.add_argument('--out_tractogram',
+                   help='Output tractogram (.trk). Required for any mutation.')
+
     add_args = p.add_argument_group('Add operation',
                                     'Requires the out_tractogram argument.')
     add_args.add_argument('--add_dps_file',
                           help='File containing the data to add to\n'
-                               'streamlines.')
+                               'streamlines (.txt, .npy or .mat).')
     add_args.add_argument('--add_dps_key', type=str,
                           help='Where to store the data in the tractogram.')
 
@@ -56,16 +59,13 @@ def _build_arg_parser():
                              help='Where to find the data to be deleted, in\n'
                                   'the tractogram.')
 
-    p.add_argument('--out_tractogram',
-                   help='Output tractogram (.trk). Required for any mutation.')
-
     export_args = p.add_argument_group('Export operation')
     export_args.add_argument('--export_dps_key', type=str,
                              help='Where to find the data to be exported,\n'
                                   'in the tractogram.')
     export_args.add_argument('--export_dps_file',
                              help='File in which the extracted data will be\n'
-                                  'saved.')
+                                  'saved (.txt or .npy).')
 
     add_verbose_arg(p)
     add_overwrite_arg(p)
@@ -116,10 +116,10 @@ def main():
 
     if args.operation == 'export':
         # Extract data and reshape
-        if not args.export_dps_key in sft.data_per_streamline.keys():
+        if args.export_dps_key not in sft.data_per_streamline.keys():
             raise ValueError('Data does not have any data_per_streamline'
                              ' entry stored at this key: {}'
-                                .format(args.export_dps_key))
+                             .format(args.export_dps_key))
 
         data = np.squeeze(sft.data_per_streamline[args.export_dps_key])
         save_matrix_in_any_format(args.export_dps_file, data)

From da0c8eb64509e244f8612057e8af2e4099b9270a Mon Sep 17 00:00:00 2001
From: VincentBeaud <vincent.beaudoin@icloud.com>
Date: Mon, 2 Dec 2024 16:06:55 -0500
Subject: [PATCH 04/10] Make dps_key mandatory + tests

---
 scripts/scil_tractogram_dps_math.py       | 37 ++++++++++-------------
 scripts/tests/test_tractogram_dps_math.py | 36 +++++++++++-----------
 2 files changed, 34 insertions(+), 39 deletions(-)

diff --git a/scripts/scil_tractogram_dps_math.py b/scripts/scil_tractogram_dps_math.py
index 3cd142461..30432b093 100755
--- a/scripts/scil_tractogram_dps_math.py
+++ b/scripts/scil_tractogram_dps_math.py
@@ -37,10 +37,13 @@ def _build_arg_parser():
     p.add_argument('operation', metavar='OPERATION',
                    choices=['add', 'delete', 'export'],
                    help='The type of operation to be performed on the\n'
-                        'tractogram\'s data_per_streamline. Must be one of\n'
-                        'the following: [%(choices)s]. The arguments\n'
-                        'required for each operation are specified under\n'
-                        'each group below.')
+                        'tractogram\'s data_per_streamline at the given\n'
+                        'key. Must be one of the following: [%(choices)s].\n'
+                        'The additional arguments required for each\n'
+                        'operation are specified under each group below.')
+    p.add_argument('dps_key', type=str,
+                   help='Where to find the data to be exported,\n'
+                        'in the tractogram.')
 
     p.add_argument('--out_tractogram',
                    help='Output tractogram (.trk). Required for any mutation.')
@@ -50,19 +53,11 @@ def _build_arg_parser():
     add_args.add_argument('--add_dps_file',
                           help='File containing the data to add to\n'
                                'streamlines (.txt, .npy or .mat).')
-    add_args.add_argument('--add_dps_key', type=str,
-                          help='Where to store the data in the tractogram.')
 
-    delete_args = p.add_argument_group('Delete operation',
-                                       'Requires the out_tractogram argument.')
-    delete_args.add_argument('--delete_dps_key', type=str,
-                             help='Where to find the data to be deleted, in\n'
-                                  'the tractogram.')
+    _ = p.add_argument_group('Delete operation',
+                             'Requires the out_tractogram argument.')
 
     export_args = p.add_argument_group('Export operation')
-    export_args.add_argument('--export_dps_key', type=str,
-                             help='Where to find the data to be exported,\n'
-                                  'in the tractogram.')
     export_args.add_argument('--export_dps_file',
                              help='File in which the extracted data will be\n'
                                   'saved (.txt or .npy).')
@@ -91,10 +86,10 @@ def main():
 
     if args.operation == 'add':
         # Make sure the user is not unwillingly overwritting dps
-        if (args.add_dps_key in sft.get_data_per_streamline_keys() and
+        if (args.dps_key in sft.get_data_per_streamline_keys() and
                 not args.overwrite):
             parser.error('"{}" already in data per streamline. Use -f to force'
-                         ' overwriting.'.format(args.add_dps_key))
+                         ' overwriting.'.format(args.dps_key))
 
         # Load data and remove extraneous dimensions
         data = np.squeeze(load_matrix_in_any_format(args.add_dps_file))
@@ -105,23 +100,23 @@ def main():
                              ' streamlines ({}).'.format(data.shape[0],
                                                          len(sft)))
 
-        sft.data_per_streamline[args.add_dps_key] = data
+        sft.data_per_streamline[args.dps_key] = data
 
         save_tractogram(sft, args.out_tractogram)
 
     if args.operation == 'delete':
-        del sft.data_per_streamline[args.delete_dps_key]
+        del sft.data_per_streamline[args.dps_key]
 
         save_tractogram(sft, args.out_tractogram)
 
     if args.operation == 'export':
         # Extract data and reshape
-        if args.export_dps_key not in sft.data_per_streamline.keys():
+        if args.dps_key not in sft.data_per_streamline.keys():
             raise ValueError('Data does not have any data_per_streamline'
                              ' entry stored at this key: {}'
-                             .format(args.export_dps_key))
+                             .format(args.dps_key))
 
-        data = np.squeeze(sft.data_per_streamline[args.export_dps_key])
+        data = np.squeeze(sft.data_per_streamline[args.dps_key])
         save_matrix_in_any_format(args.export_dps_file, data)
 
 
diff --git a/scripts/tests/test_tractogram_dps_math.py b/scripts/tests/test_tractogram_dps_math.py
index 531fb8459..6a4e5e007 100644
--- a/scripts/tests/test_tractogram_dps_math.py
+++ b/scripts/tests/test_tractogram_dps_math.py
@@ -29,9 +29,9 @@ def test_execution_dps_math_add(script_runner, monkeypatch):
     filename = 'vals.npy'
     outname = 'out.trk'
     np.save(filename, np.arange(len(sft)))
-    ret = script_runner.run('scil_tractogram_dps_math.py', in_bundle, 'add',
+    ret = script_runner.run('scil_tractogram_dps_math.py',
+                            in_bundle, 'add', 'key',
                             '--add_dps_file', filename,
-                            '--add_dps_key', 'key',
                             '--out_tractogram', outname,
                             '-f')
     assert ret.success
@@ -45,9 +45,9 @@ def test_execution_dps_math_add_with_missing_vals(script_runner, monkeypatch):
     filename = 'vals.npy'
     outname = 'out.trk'
     np.save(filename, np.arange(len(sft) - 10))
-    ret = script_runner.run('scil_tractogram_dps_math.py', in_bundle, 'add',
+    ret = script_runner.run('scil_tractogram_dps_math.py',
+                            in_bundle, 'add', 'key',
                             '--add_dps_file', filename,
-                            '--add_dps_key', 'key',
                             '--out_tractogram', outname,
                             '-f')
     assert ret.stderr
@@ -62,15 +62,15 @@ def test_execution_dps_math_add_with_existing_key(script_runner, monkeypatch):
     outname = 'out.trk'
     outname2 = 'out_2.trk'
     np.save(filename, np.arange(len(sft)))
-    ret = script_runner.run('scil_tractogram_dps_math.py', in_bundle, 'add',
+    ret = script_runner.run('scil_tractogram_dps_math.py',
+                            in_bundle, 'add', 'key',
                             '--add_dps_file', filename,
-                            '--add_dps_key', 'key',
                             '--out_tractogram', outname,
                             '-f')
     assert ret.success
-    ret = script_runner.run('scil_tractogram_dps_math.py', outname, 'add',
+    ret = script_runner.run('scil_tractogram_dps_math.py',
+                            outname, 'add', 'key',
                             '--add_dps_file', filename,
-                            '--add_dps_key', 'key',
                             '--out_tractogram', outname2,)
     assert not ret.success
 
@@ -83,9 +83,9 @@ def test_execution_dps_math_tck(script_runner, monkeypatch):
     filename = 'vals.npy'
     outname = 'out.tck'
     np.save(filename, np.arange(len(sft)))
-    ret = script_runner.run('scil_tractogram_dps_math.py', in_bundle, 'add',
+    ret = script_runner.run('scil_tractogram_dps_math.py',
+                            in_bundle, 'add', 'key',
                             '--add_dps_file', filename,
-                            '--add_dps_key', 'key',
                             '--out_tractogram', outname,
                             '-f')
     assert not ret.success
@@ -102,8 +102,8 @@ def test_execution_dps_math_delete(script_runner, monkeypatch):
     }
     save_tractogram(sft, in_bundle)
     outname = 'out.trk'
-    ret = script_runner.run('scil_tractogram_dps_math.py', in_bundle, 'delete',
-                            '--delete_dps_key', 'key',
+    ret = script_runner.run('scil_tractogram_dps_math.py',
+                            in_bundle, 'delete', 'key',
                             '--out_tractogram', outname,
                             '-f')
     assert ret.success
@@ -114,8 +114,8 @@ def test_execution_dps_math_delete_no_key(script_runner, monkeypatch):
     in_bundle = os.path.join(SCILPY_HOME, 'filtering',
                              'bundle_4.trk')
     outname = 'out.trk'
-    ret = script_runner.run('scil_tractogram_dps_math.py', in_bundle, 'delete',
-                            '--delete_dps_key', 'key',
+    ret = script_runner.run('scil_tractogram_dps_math.py',
+                            in_bundle, 'delete', 'key',
                             '--out_tractogram', outname,
                             '-f')
     assert not ret.success
@@ -132,8 +132,8 @@ def test_execution_dps_math_export(script_runner, monkeypatch):
     }
     save_tractogram(sft, in_bundle)
     filename = 'out.txt'
-    ret = script_runner.run('scil_tractogram_dps_math.py', in_bundle, 'export',
-                            '--export_dps_key', 'key',
+    ret = script_runner.run('scil_tractogram_dps_math.py',
+                            in_bundle, 'export', 'key',
                             '--export_dps_file', filename,
                             '-f')
     assert ret.success
@@ -144,8 +144,8 @@ def test_execution_dps_math_export_no_key(script_runner, monkeypatch):
     in_bundle = os.path.join(SCILPY_HOME, 'filtering',
                              'bundle_4.trk')
     filename = 'out.txt'
-    ret = script_runner.run('scil_tractogram_dps_math.py', in_bundle, 'export',
-                            '--export_dps_key', 'key',
+    ret = script_runner.run('scil_tractogram_dps_math.py',
+                            in_bundle, 'export', 'key',
                             '--export_dps_file', filename,
                             '-f')
     assert not ret.success

From f9695cd37790e0dd6f18f38638b54b052dcf4753 Mon Sep 17 00:00:00 2001
From: VincentBeaud <vincent.beaudoin@icloud.com>
Date: Tue, 10 Dec 2024 10:52:33 -0500
Subject: [PATCH 05/10] Clarify script doc

---
 scripts/scil_tractogram_dps_math.py | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/scripts/scil_tractogram_dps_math.py b/scripts/scil_tractogram_dps_math.py
index 30432b093..b915448e3 100755
--- a/scripts/scil_tractogram_dps_math.py
+++ b/scripts/scil_tractogram_dps_math.py
@@ -2,15 +2,20 @@
 # -*- coding: utf-8 -*-
 
 """
-Add, extract or delete information to each streamline from a tractogram
+Add, extract or delete dps (data_per_streamline) information to a tractogram
 file. Can be for example SIFT2 weights, processing information, bundle IDs,
 tracking seeds, etc.
 
-Input and output tractograms must always be .trk to simplify filetype checks
-for each operation.
+Input and output tractograms must always be .trk. If you wish to add dps to
+a .tck file, please convert it to .trk first using scil_tractogram_convert.py.
+
+Usage examples:
+    > scil_tractogram_dps_math.py tractogram.trk add "bundle_ids"
+        --add_dps_file my_bundle_ids.txt
+    > scil_tractogram_dps_math.py tractogram.trk export "seeds"
+        --export_dps_file seeds.npy
 """
 
-import os
 import argparse
 import logging
 

From 0cbfce3b632f5308ad4575cb89871396b512a9ac Mon Sep 17 00:00:00 2001
From: VincentBeaud <vincent.beaudoin@icloud.com>
Date: Wed, 11 Dec 2024 11:04:34 -0500
Subject: [PATCH 06/10] Argument checks, pep8 and tests

---
 scilpy/io/streamlines.py                  |  4 +-
 scripts/scil_tractogram_dps_math.py       | 78 ++++++++++++++---------
 scripts/tests/test_tractogram_dps_math.py | 34 +++++-----
 3 files changed, 69 insertions(+), 47 deletions(-)

diff --git a/scilpy/io/streamlines.py b/scilpy/io/streamlines.py
index cf26c85cc..0fc196f6a 100644
--- a/scilpy/io/streamlines.py
+++ b/scilpy/io/streamlines.py
@@ -75,8 +75,8 @@ def load_tractogram_with_reference(parser, args, filepath, arg_name=None):
     filepath: str
         Path of the tractogram file.
     arg_name: str, optional
-        Name of the reference argument. By default the args.ref is used. If
-        arg_name is given, then args.arg_name_ref will be used instead.
+        Name of the reference argument. By default the args.reference is used.
+        If arg_name is given, then args.arg_name_ref will be used instead.
     """
     if is_argument_set(args, 'bbox_check'):
         bbox_check = args.bbox_check
diff --git a/scripts/scil_tractogram_dps_math.py b/scripts/scil_tractogram_dps_math.py
index b915448e3..5b96a5827 100755
--- a/scripts/scil_tractogram_dps_math.py
+++ b/scripts/scil_tractogram_dps_math.py
@@ -2,24 +2,26 @@
 # -*- coding: utf-8 -*-
 
 """
-Add, extract or delete dps (data_per_streamline) information to a tractogram
+Import, extract or delete dps (data_per_streamline) information to a tractogram
 file. Can be for example SIFT2 weights, processing information, bundle IDs,
 tracking seeds, etc.
 
-Input and output tractograms must always be .trk. If you wish to add dps to
-a .tck file, please convert it to .trk first using scil_tractogram_convert.py.
+Input and output tractograms must be .trk, unless you are using the 'import'
+operation, in which case a .tck input tractogram is accepted.
 
 Usage examples:
-    > scil_tractogram_dps_math.py tractogram.trk add "bundle_ids"
-        --add_dps_file my_bundle_ids.txt
+    > scil_tractogram_dps_math.py tractogram.trk import "bundle_ids"
+        --in_dps_file my_bundle_ids.txt
     > scil_tractogram_dps_math.py tractogram.trk export "seeds"
-        --export_dps_file seeds.npy
+        --out_dps_file seeds.npy
 """
 
+import nibabel as nib
 import argparse
 import logging
 
 from dipy.io.streamline import save_tractogram, load_tractogram
+from scilpy.io.streamlines import load_tractogram_with_reference
 import numpy as np
 
 from scilpy.io.utils import (add_overwrite_arg,
@@ -38,32 +40,29 @@ def _build_arg_parser():
         formatter_class=argparse.RawTextHelpFormatter)
 
     p.add_argument('in_tractogram',
-                   help='Input tractogram (.trk).')
+                   help='Input tractogram (.trk for all operations,'
+                        '.tck accepted for import).')
     p.add_argument('operation', metavar='OPERATION',
-                   choices=['add', 'delete', 'export'],
+                   choices=['import', 'delete', 'export'],
                    help='The type of operation to be performed on the\n'
                         'tractogram\'s data_per_streamline at the given\n'
                         'key. Must be one of the following: [%(choices)s].\n'
                         'The additional arguments required for each\n'
                         'operation are specified under each group below.')
     p.add_argument('dps_key', type=str,
-                   help='Where to find the data to be exported,\n'
-                        'in the tractogram.')
+                   help='Key name used for the operation.')
 
     p.add_argument('--out_tractogram',
-                   help='Output tractogram (.trk). Required for any mutation.')
+                   help='Output tractogram (.trk). Required for "import" and\n'
+                        '"delete" operations.')
 
-    add_args = p.add_argument_group('Add operation',
-                                    'Requires the out_tractogram argument.')
-    add_args.add_argument('--add_dps_file',
-                          help='File containing the data to add to\n'
-                               'streamlines (.txt, .npy or .mat).')
+    import_args = p.add_argument_group('Operation "import" mandatory options')
+    import_args.add_argument('--in_dps_file',
+                             help='File containing the data to import to\n'
+                                  'streamlines (.txt, .npy or .mat).')
 
-    _ = p.add_argument_group('Delete operation',
-                             'Requires the out_tractogram argument.')
-
-    export_args = p.add_argument_group('Export operation')
-    export_args.add_argument('--export_dps_file',
+    export_args = p.add_argument_group('Operation "export" mandatory options')
+    export_args.add_argument('--out_dps_file',
                              help='File in which the extracted data will be\n'
                                   'saved (.txt or .npy).')
 
@@ -78,18 +77,31 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    check_tract_trk(parser, args.in_tractogram)
+    if args.operation == 'import':
+        if not nib.streamlines.is_supported(args.in_tractogram):
+            parser.error('Invalid input streamline file format (must be trk ' +
+                         'or tck): {0}'.format(args.in_tractogram))
+    else:
+        check_tract_trk(parser, args.in_tractogram)
+
     if args.out_tractogram:
         check_tract_trk(parser, args.out_tractogram)
 
-    # I/O assertions
-    assert_inputs_exist(parser, args.in_tractogram, args.add_dps_file)
-    assert_outputs_exist(parser, args, [], optional=[args.export_dps_file,
+    assert_inputs_exist(parser, args.in_tractogram, args.in_dps_file)
+    assert_outputs_exist(parser, args, [], optional=[args.out_dps_file,
                                                      args.out_tractogram])
 
-    sft = load_tractogram(args.in_tractogram, 'same')
+    sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
+
+    if args.operation == 'import':
+        if args.in_dps_file is None:
+            parser.error('The --in_dps_file option is required for ' +
+                         'the "import" operation.')
+
+        if args.out_tractogram is None:
+            parser.error('The --out_tractogram option is required for ' +
+                         'the "import" operation.')
 
-    if args.operation == 'add':
         # Make sure the user is not unwillingly overwritting dps
         if (args.dps_key in sft.get_data_per_streamline_keys() and
                 not args.overwrite):
@@ -97,7 +109,7 @@ def main():
                          ' overwriting.'.format(args.dps_key))
 
         # Load data and remove extraneous dimensions
-        data = np.squeeze(load_matrix_in_any_format(args.add_dps_file))
+        data = np.squeeze(load_matrix_in_any_format(args.in_dps_file))
 
         # Quick check as the built-in error from sft is not too explicit
         if len(sft) != data.shape[0]:
@@ -110,11 +122,19 @@ def main():
         save_tractogram(sft, args.out_tractogram)
 
     if args.operation == 'delete':
+        if args.out_tractogram is None:
+            parser.error('The --out_tractogram option is required for ' +
+                         'the "delete" operation.')
+
         del sft.data_per_streamline[args.dps_key]
 
         save_tractogram(sft, args.out_tractogram)
 
     if args.operation == 'export':
+        if args.out_dps_file is None:
+            parser.error('The --out_dps_file option is required for ' +
+                         'the "export" operation.')
+
         # Extract data and reshape
         if args.dps_key not in sft.data_per_streamline.keys():
             raise ValueError('Data does not have any data_per_streamline'
@@ -122,7 +142,7 @@ def main():
                              .format(args.dps_key))
 
         data = np.squeeze(sft.data_per_streamline[args.dps_key])
-        save_matrix_in_any_format(args.export_dps_file, data)
+        save_matrix_in_any_format(args.out_dps_file, data)
 
 
 if __name__ == '__main__':
diff --git a/scripts/tests/test_tractogram_dps_math.py b/scripts/tests/test_tractogram_dps_math.py
index 6a4e5e007..03b758de2 100644
--- a/scripts/tests/test_tractogram_dps_math.py
+++ b/scripts/tests/test_tractogram_dps_math.py
@@ -21,7 +21,7 @@ def test_help_option(script_runner):
     assert ret.success
 
 
-def test_execution_dps_math_add(script_runner, monkeypatch):
+def test_execution_dps_math_import(script_runner, monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
     in_bundle = os.path.join(SCILPY_HOME, 'filtering',
                              'bundle_4.trk')
@@ -30,14 +30,15 @@ def test_execution_dps_math_add(script_runner, monkeypatch):
     outname = 'out.trk'
     np.save(filename, np.arange(len(sft)))
     ret = script_runner.run('scil_tractogram_dps_math.py',
-                            in_bundle, 'add', 'key',
-                            '--add_dps_file', filename,
+                            in_bundle, 'import', 'key',
+                            '--in_dps_file', filename,
                             '--out_tractogram', outname,
                             '-f')
     assert ret.success
 
 
-def test_execution_dps_math_add_with_missing_vals(script_runner, monkeypatch):
+def test_execution_dps_math_import_with_missing_vals(script_runner,
+                                                     monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
     in_bundle = os.path.join(SCILPY_HOME, 'filtering',
                              'bundle_4.trk')
@@ -46,14 +47,15 @@ def test_execution_dps_math_add_with_missing_vals(script_runner, monkeypatch):
     outname = 'out.trk'
     np.save(filename, np.arange(len(sft) - 10))
     ret = script_runner.run('scil_tractogram_dps_math.py',
-                            in_bundle, 'add', 'key',
-                            '--add_dps_file', filename,
+                            in_bundle, 'import', 'key',
+                            '--in_dps_file', filename,
                             '--out_tractogram', outname,
                             '-f')
     assert ret.stderr
 
 
-def test_execution_dps_math_add_with_existing_key(script_runner, monkeypatch):
+def test_execution_dps_math_import_with_existing_key(script_runner,
+                                                     monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
     in_bundle = os.path.join(SCILPY_HOME, 'filtering',
                              'bundle_4.trk')
@@ -63,19 +65,19 @@ def test_execution_dps_math_add_with_existing_key(script_runner, monkeypatch):
     outname2 = 'out_2.trk'
     np.save(filename, np.arange(len(sft)))
     ret = script_runner.run('scil_tractogram_dps_math.py',
-                            in_bundle, 'add', 'key',
-                            '--add_dps_file', filename,
+                            in_bundle, 'import', 'key',
+                            '--in_dps_file', filename,
                             '--out_tractogram', outname,
                             '-f')
     assert ret.success
     ret = script_runner.run('scil_tractogram_dps_math.py',
-                            outname, 'add', 'key',
-                            '--add_dps_file', filename,
+                            outname, 'import', 'key',
+                            '--in_dps_file', filename,
                             '--out_tractogram', outname2,)
     assert not ret.success
 
 
-def test_execution_dps_math_tck(script_runner, monkeypatch):
+def test_execution_dps_math_tck_output(script_runner, monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
     in_bundle = os.path.join(SCILPY_HOME, 'filtering',
                              'bundle_4.trk')
@@ -84,8 +86,8 @@ def test_execution_dps_math_tck(script_runner, monkeypatch):
     outname = 'out.tck'
     np.save(filename, np.arange(len(sft)))
     ret = script_runner.run('scil_tractogram_dps_math.py',
-                            in_bundle, 'add', 'key',
-                            '--add_dps_file', filename,
+                            in_bundle, 'import', 'key',
+                            '--in_dps_file', filename,
                             '--out_tractogram', outname,
                             '-f')
     assert not ret.success
@@ -134,7 +136,7 @@ def test_execution_dps_math_export(script_runner, monkeypatch):
     filename = 'out.txt'
     ret = script_runner.run('scil_tractogram_dps_math.py',
                             in_bundle, 'export', 'key',
-                            '--export_dps_file', filename,
+                            '--out_dps_file', filename,
                             '-f')
     assert ret.success
 
@@ -146,6 +148,6 @@ def test_execution_dps_math_export_no_key(script_runner, monkeypatch):
     filename = 'out.txt'
     ret = script_runner.run('scil_tractogram_dps_math.py',
                             in_bundle, 'export', 'key',
-                            '--export_dps_file', filename,
+                            '--out_dps_file', filename,
                             '-f')
     assert not ret.success

From 36d0aa338abaeca13f892d060401d5f8f8628271 Mon Sep 17 00:00:00 2001
From: VincentBeaud <vincent.beaudoin@icloud.com>
Date: Thu, 12 Dec 2024 09:51:53 -0500
Subject: [PATCH 07/10] Avoid scalar with dim > 0 by squeezing. Passes test and
 pep8 no warning.

---
 scilpy/tractograms/dps_and_dpp_management.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scilpy/tractograms/dps_and_dpp_management.py b/scilpy/tractograms/dps_and_dpp_management.py
index bf40e4350..5390bf063 100644
--- a/scilpy/tractograms/dps_and_dpp_management.py
+++ b/scilpy/tractograms/dps_and_dpp_management.py
@@ -217,7 +217,7 @@ def project_dpp_to_map(sft, dpp_key, sum_lines=False, endpoints_only=False):
         for p in points:
             x, y, z = sft.streamlines[s][p, :].astype(int)  # Or floor
             count[x, y, z] += 1
-            the_map[x, y, z] += sft.data_per_point[dpp_key][s][p]
+            the_map[x, y, z] += np.squeeze(sft.data_per_point[dpp_key][s][p])
 
     if not sum_lines:
         count = np.maximum(count, 1e-6)  # Avoid division by 0

From 66d36c6d8301dea7149029fc42f7dfc637079cb0 Mon Sep 17 00:00:00 2001
From: karp2601 <karp2601@dinf-0051-20b.DInf.fsci.usherbrooke.ca>
Date: Thu, 12 Dec 2024 09:58:13 -0500
Subject: [PATCH 08/10] Fixing chekc in script and adding test

---
 scripts/scil_NODDI_maps.py       |  7 ++++---
 scripts/tests/test_NODDI_maps.py | 22 ++++++++++++++++++++--
 2 files changed, 24 insertions(+), 5 deletions(-)

diff --git a/scripts/scil_NODDI_maps.py b/scripts/scil_NODDI_maps.py
index 96be2f227..2d067c5ff 100755
--- a/scripts/scil_NODDI_maps.py
+++ b/scripts/scil_NODDI_maps.py
@@ -120,12 +120,13 @@ def main():
     shells_centroids, indices_shells = identify_shells(bvals, args.tolerance,
                                                        round_centroids=True)
 
-    nb_shells = len(shells_centroids)
+    non_b0_shells = shells_centroids[shells_centroids > args.tolerance]
+    nb_shells = len(non_b0_shells)
     if nb_shells <= 1:
         raise ValueError("Amico's NODDI works with data with more than one "
                          "shell, but you seem to have single-shell data (we "
-                         "found shells {}). Change tolerance if necessary."
-                         .format(np.sort(shells_centroids)))
+                         "found shell {}). Change tolerance if necessary."
+                         .format(non_b0_shells[0]))
 
     logging.info('Will compute NODDI with AMICO on {} shells at found at {}.'
                  .format(len(shells_centroids), np.sort(shells_centroids)))
diff --git a/scripts/tests/test_NODDI_maps.py b/scripts/tests/test_NODDI_maps.py
index 105bb72e6..ed7e66b9f 100644
--- a/scripts/tests/test_NODDI_maps.py
+++ b/scripts/tests/test_NODDI_maps.py
@@ -8,7 +8,8 @@
 from scilpy.io.fetcher import fetch_data, 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=['commit_amico.zip',
+                                           'processing.zip'])
 tmp_dir = tempfile.TemporaryDirectory()
 
 
@@ -32,5 +33,22 @@ def test_execution_commit_amico(script_runner, monkeypatch):
                             '--out_dir', 'noddi', '--tol', '30',
                             '--para_diff', '0.0017', '--iso_diff', '0.003',
                             '--lambda1', '0.5', '--lambda2', '0.001',
-                            '--processes', '1')
+                            '--processes', '1', '-f')
     assert ret.success
+
+
+def test_single_shell_fail(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_dwi = os.path.join(SCILPY_HOME, 'processing',
+                          'dwi_crop_1000.nii.gz')
+    in_bval = os.path.join(SCILPY_HOME, 'processing',
+                           '1000.bval')
+    in_bvec = os.path.join(SCILPY_HOME, 'processing',
+                           '1000.bvec')
+    ret = script_runner.run('scil_NODDI_maps.py', in_dwi,
+                            in_bval, in_bvec,
+                            '--out_dir', 'noddi', '--tol', '30',
+                            '--para_diff', '0.0017', '--iso_diff', '0.003',
+                            '--lambda1', '0.5', '--lambda2', '0.001',
+                            '--processes', '1', '-f')
+    assert not ret.success

From 60903adb3284e8587bbcb346be52967b629de705 Mon Sep 17 00:00:00 2001
From: VincentBeaud <vincent.beaudoin@icloud.com>
Date: Thu, 12 Dec 2024 10:09:37 -0500
Subject: [PATCH 09/10] Clarify doc to differentiate dpp_math with dps mode and
 dps_math

---
 scripts/scil_tractogram_dpp_math.py | 3 ++-
 scripts/scil_tractogram_dps_math.py | 4 ++++
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/scripts/scil_tractogram_dpp_math.py b/scripts/scil_tractogram_dpp_math.py
index 9303c1d32..5949fddb6 100755
--- a/scripts/scil_tractogram_dpp_math.py
+++ b/scripts/scil_tractogram_dpp_math.py
@@ -19,7 +19,8 @@
 
 If endpoints_only and dps mode is set operation will be calculated across the
 data at the endpoints and stored as a single value (or array in the 4D case)
-per streamline.
+per streamline. If you wish to perform operations on dps values, please use
+scil_tractogram_dps_math.py.
 
 Endpoint only operation:
 correlation: correlation calculated between arrays extracted from streamline
diff --git a/scripts/scil_tractogram_dps_math.py b/scripts/scil_tractogram_dps_math.py
index 5b96a5827..02837e07d 100755
--- a/scripts/scil_tractogram_dps_math.py
+++ b/scripts/scil_tractogram_dps_math.py
@@ -6,6 +6,10 @@
 file. Can be for example SIFT2 weights, processing information, bundle IDs,
 tracking seeds, etc.
 
+This script is not the same as the dps mode of scil_tractogram_dpp_math.py,
+which performs operations on dpp (data_per_point) and saves the result as dps.
+Instead this script performs operations directly on dps values.
+
 Input and output tractograms must be .trk, unless you are using the 'import'
 operation, in which case a .tck input tractogram is accepted.
 

From e63c833787db641cc872b790a1025106aa068a54 Mon Sep 17 00:00:00 2001
From: karp2601 <karp2601@dinf-0051-20b.DInf.fsci.usherbrooke.ca>
Date: Thu, 12 Dec 2024 10:26:55 -0500
Subject: [PATCH 10/10] Adding ref to freewater

---
 scripts/scil_freewater_maps.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/scripts/scil_freewater_maps.py b/scripts/scil_freewater_maps.py
index f24c3a94f..854eb30ab 100755
--- a/scripts/scil_freewater_maps.py
+++ b/scripts/scil_freewater_maps.py
@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 
 """
-Compute Free Water maps [1] using AMICO.
+Compute Free Water maps [1] using the AMICO framework [2].
 This script supports both single and multi-shell data.
 
 Formerly: scil_compute_freewater.py
@@ -35,6 +35,9 @@
     [1] Pasternak 0, Sochen N, Gur Y, Intrator N, Assaf Y.
         Free water elimination and mapping from diffusion mri.
         Magn Reson Med. 62 (3) (2009) 717-730.
+    [2] Daducci A, et al. Accelerated microstructure imaging
+        via convex optimization (AMICO) from diffusion MRI data.
+        Neuroimage 105 (2015) 32-44.
 """