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Unit test: segment_tractogram #1290

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11d0079
Add unit test for segment_tractogram_from_roi. Runs, checks nothing
EmmaRenauld Dec 2, 2025
7375d1a
checks ok!
EmmaRenauld Dec 2, 2025
5f92af1
Works with WPC and IC and NC too
EmmaRenauld Dec 3, 2025
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22 changes: 11 additions & 11 deletions src/scilpy/cli/scil_tractogram_segment_with_ROI_and_score.py
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Original file line number Diff line number Diff line change
Expand Up @@ -239,26 +239,24 @@ def load_and_verify_everything(parser, args):
logging.info("Loading and/or computing ground-truth masks, limits "
"masks and any_masks.")
gt_masks = compute_masks_from_bundles(gt_masks_files, parser, args)
inv_all_masks = compute_masks_from_bundles(all_masks_files, parser, args,
inverse_mask=True)
all_masks = compute_masks_from_bundles(all_masks_files, parser, args)
any_masks = compute_masks_from_bundles(any_masks_files, parser, args)

logging.info("Extracting ground-truth head and tail masks.")
gt_tails, gt_heads = compute_endpoint_masks(roi_options, args.out_dir)

# Update the list of every ROI, remove duplicates
# Check that all ROIs are compatible (remove duplicates)
logging.info("Verifying tractogram compatibility with endpoint ROIs.")
list_rois = gt_tails + gt_heads
list_rois = list(dict.fromkeys(list_rois)) # Removes duplicates

logging.info("Verifying tractogram compatibility with endpoint ROIs.")
for file in list_rois:
compatible = is_header_compatible(sft, file)
if not compatible:
parser.error("Input tractogram incompatible with {}".format(file))

return (gt_tails, gt_heads, sft, bundle_names, list_rois,
return (gt_tails, gt_heads, sft, bundle_names,
lengths, angles, orientation_lengths, abs_orientation_lengths,
inv_all_masks, gt_masks, any_masks, dimensions, json_outputs)
all_masks, gt_masks, any_masks, dimensions, json_outputs)


def read_config_file(args):
Expand Down Expand Up @@ -428,17 +426,19 @@ def main():
logging.getLogger().setLevel(logging.getLevelName(args.verbose))

# Load
(gt_tails, gt_heads, sft, bundle_names, list_rois, bundle_lengths, angles,
orientation_lengths, abs_orientation_lengths, inv_all_masks, gt_masks,
(gt_tails, gt_heads, sft, bundle_names, bundle_lengths, angles,
orientation_lengths, abs_orientation_lengths, all_masks, gt_masks,
any_masks, dimensions,
json_outputs) = load_and_verify_everything(parser, args)

# Segment VB, WPC, IB
(vb_sft_list, wpc_sft_list, ib_sft_list, nc_sft,
ib_names, bundle_stats) = segment_tractogram_from_roi(
sft, gt_tails, gt_heads, bundle_names, bundle_lengths, angles,
orientation_lengths, abs_orientation_lengths, inv_all_masks, any_masks,
list_rois, args)
orientation_lengths, abs_orientation_lengths, all_masks, any_masks,
args.out_dir, args.compute_ic, args.save_wpc_separately, args.unique,
args.remove_wpc_belonging_to_another_bundle,
args.no_empty, args.bbox_check, args.dilate_endpoints)

# Save results
with open(json_outputs[0], "w") as f:
Expand Down
145 changes: 142 additions & 3 deletions src/scilpy/segment/tests/test_tractogram_from_roi.py
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Original file line number Diff line number Diff line change
@@ -1,14 +1,153 @@
import logging
import os
import tempfile

from dipy.io.stateful_tractogram import Space, StatefulTractogram, Origin
import nibabel as nib
import numpy as np

from numpy.testing import (assert_array_equal,
assert_equal)

from scilpy.segment.tractogram_from_roi import (_extract_vb_one_bundle,
_extract_ib_one_bundle)
from dipy.io.stateful_tractogram import Space, StatefulTractogram
_extract_ib_one_bundle,
segment_tractogram_from_roi)


def test_compute_masks_from_bundles():
pass

def test_compute_endpoint_masks():
pass

def test_segment_tractogram_from_roi():

# Creating an example.
# This is already pretty complex, we will not test all complex
# configurations
# Inventing a volume of size 5, 5, 5 and bundles. See ROIs below.
# ROIs are y=0, y=4, z=0, z=4 slices.

# Bundle 1: left to right (in y). Start at y=0, finish at y=4.
# - two streamlines, reversed
# - any mask: need to pass in voxel [1, 1, 1]
streamline_r_to_l = [[1.1, 0.2, 1.3],
[1.1, 2.2, 1.4],
[1.1, 3.3, 1.3],
[1.1, 4.3, 1.2]]
streamline_l_to_r = streamline_r_to_l[::-1]
bundle1_any_mask = np.zeros((5, 5, 5))
bundle1_any_mask[1, 1, 1] = 1 # No real point there but they pass through
# wpc not passing by [1, 1, 1]
wpc_streamline1 = [[2.1, 0.2, 1.3],
[2.1, 2.2, 1.4],
[2.1, 3.3, 1.3],
[2.1, 4.3, 1.2]]

# Bundle 2: vertical. Starts at z=0. Finishes at z=4.
streamline_vertical = [[3.4, 5.9, 0.9],
[3.5, 1.8, 1.8],
[3.4, 2.7, 2.6],
[3.4, 4.7, 4.5]]
bundle2_all_mask = np.zeros((5, 5, 5))
bundle2_all_mask[3, :, :] = 1
# wpc not entirely in [3, :, :]
wpc_streamline2 = [[3.4, 5.9, 0.9],
[3.5, 1.8, 1.8],
[5.4, 2.7, 2.6],
[3.4, 4.7, 4.5]]

# Adding an IC streamline. From y=0, but reaches z=0 instead of reaching
# y=4
ic_streamline = [[1.1, 0.2, 1.3],
[1.1, 2.2, 1.4],
[1.1, 3.3, 1.3],
[1.1, 2.3, 0.2]]

# Adding a NC streamline. Finishes in the middle of the volume, so not in
# any ROI.
nc_streamline = [[1.1, 0.2, 1.3],
[1.1, 2.2, 1.4],
[1.1, 3.3, 1.3],
[3.1, 2.3, 3.2]]

# Preparing data.
gt_heads = [] # will be prepared below
gt_tails = [] # Will be prepared below
bundle_names = ['l-r', 'vertical']
lengths = [None, None]
angles = [359, 359]
orientation_length = [None, None]
abs_orientation_length = [None, None]
all_masks = [None, bundle2_all_mask]
any_masks = [bundle1_any_mask, None]

# Many things must be saved on disk.
with tempfile.TemporaryDirectory() as tmpdirname:
print(f'Created temporary directory: {tmpdirname}')

fake_ref = nib.Nifti1Image(np.zeros((5, 5, 5)), affine=np.eye(4))
sft = StatefulTractogram([streamline_r_to_l, streamline_l_to_r,
streamline_vertical, wpc_streamline1,
wpc_streamline2, ic_streamline,
nc_streamline],
space=Space.VOX, origin=Origin('corner'),
reference=fake_ref)

def save_img(array):
img = nib.Nifti1Image(array.astype('uint8'), affine=np.eye(4))
nib.save(img, filename)

# Bundle 1 : left to right (streamlines 1 and 2)
# Creating a fake ROI to the left and another to the right.
gt_head = np.zeros((5, 5, 5))
gt_head[:, 0, :] = 1
filename = os.path.join(tmpdirname, 'bundle1_head.nii.gz')
save_img(gt_head)
gt_heads.append(filename)

gt_tail = np.zeros((5, 5, 5))
gt_tail[:, 4, :] = 1
filename = os.path.join(tmpdirname, 'bundle1_tail.nii.gz')
save_img(gt_tail)
gt_tails.append(filename)

# Bundle 2: vertical (streamline 2)
# Creating a fake ROI at the bottom and another at the top
gt_head = np.zeros((5, 5, 5))
gt_head[:, :, 0] = 1
filename = os.path.join(tmpdirname, 'bundle2_head.nii.gz')
save_img(gt_head)
gt_heads.append(filename)

gt_tail = np.zeros((5, 5, 5))
gt_tail[:, :, 4] = 1
filename = os.path.join(tmpdirname, 'bundle2_tail.nii.gz')
save_img(gt_tail)
gt_tails.append(filename)

logging.getLogger().setLevel('INFO')
(vb_sft_list, wpc_sft_list, ib_sft_list, nc_sft, ib_names,
bundle_stats) = segment_tractogram_from_roi(
sft, gt_tails, gt_heads, bundle_names, lengths, angles,
orientation_length, abs_orientation_length, all_masks, any_masks,
out_dir=tmpdirname, compute_ic=True, save_wpc_separately=True)

print("bundle stats:", bundle_stats)

# 2 valid in bundle1, 1 valid in bundle 2
assert len(vb_sft_list) == 2
assert len(vb_sft_list[0]) == 2
assert len(vb_sft_list[1]) == 1

# two wpc streamlines
assert len(wpc_sft_list) == 2
assert len(wpc_sft_list[0]) == 1
assert len(wpc_sft_list[1]) == 1

# One IB with one streamline, one NC
assert len(ib_sft_list) == 1
assert len(ib_sft_list[0]) == 1
assert len(nc_sft) == 1


def test_extract_vb_one_bundle():
Expand Down
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