Begin tests and small fixes

scilus · Sep 12, 2024 · 77050ab · 77050ab
1 parent afe7e5d
commit 77050ab
Show file tree

Hide file tree

Showing 5 changed files with 49 additions and 80 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -63,6 +63,7 @@ jobs:
         with:
           name: test-coverage-${{ github.run_id }}
           retention-days: 1
+          include-hidden-files: true
           path: |
             .coverage
             .test_reports/

diff --git a/scilpy/tracking/seed.py b/scilpy/tracking/seed.py
@@ -336,7 +336,7 @@ def init_generator(self, rng_seed, numbers_to_skip):
             self.generator.random_sample(100000)
             numbers_to_skip -= 100000
         self.generator.random_sample(numbers_to_skip)
-        sampling_rng_seed = self.generator.random_integers(0, 2**32-1)
+        sampling_rng_seed = self.generator.randint(0, 2**32-1)
         self.sampling_generator = np.random.default_rng(sampling_rng_seed)
 
         return self.sampling_generator, indices

diff --git a/scripts/scil_fibertube_tracking.py b/scripts/scil_fibertube_tracking.py
@@ -224,11 +224,20 @@ def main():
                                      our_origin)
 
     logging.debug("Instantiating tracker")
+    max_nbr_seeds = args.nb_seeds_per_fiber * len(centerlines)
     if args.nb_fibers:
-        nbr_seeds = args.nb_seeds_per_fiber * args.nb_fibers
+        if args.nb_fibers > len(centerlines):
+            raise ValueError("The provided number of seeded fibers exceeds" +
+                             "the number of available fibertubes.")
+        else:
+            nbr_seeds = args.nb_seeds_per_fiber * args.nb_fibers
     else:
-        nbr_seeds = args.nb_seeds_per_fiber * len(centerlines)
+        nbr_seeds = max_nbr_seeds
 
+    if args.skip and nbr_seeds + args.skip > max_nbr_seeds:
+        raise ValueError("The number of seeds plus the number of skipped " +
+                         "seeds requires more fibertubes than there are " +
+                         "available.")
     tracker = Tracker(propagator, fake_mask, seed_generator, nbr_seeds,
                       min_nbr_pts, max_nbr_pts,
                       args.max_invalid_nb_points, 0,

diff --git a/.../test_fibertube_reconstruction_metrics.py → .../tests/test_fibertube_score_tractogram.py b/.../test_fibertube_reconstruction_metrics.py → .../tests/test_fibertube_score_tractogram.py
@@ -3,5 +3,5 @@
 
 
 def test_help_option(script_runner):
-    ret = script_runner.run('scil_fibertube_reconstruction_metrics.py', '--help')
+    ret = script_runner.run('scil_fibertube_score_tractogram.py', '--help')
     assert ret.success
diff --git a/scripts/tests/test_fibertube_tracking.py b/scripts/tests/test_fibertube_tracking.py
@@ -3,118 +3,77 @@
 
 import os
 import tempfile
-import numpy as np
+import nibabel as nib
 
 from scilpy import SCILPY_HOME
 from scilpy.io.fetcher import fetch_data, get_testing_files_dict
+from scilpy.io.streamlines import save_tractogram
+from dipy.io.stateful_tractogram import StatefulTractogram, Space, Origin
 
 # If they already exist, this only takes 5 seconds (check md5sum)
 fetch_data(get_testing_files_dict(), keys=['tractograms.zip'])
 tmp_dir = tempfile.TemporaryDirectory()
 
+def init_data():
+    streamlines = [[[4., 0., 4.], [4., 4., 8.], [6., 8., 8.], [12., 10., 8.], [4.,6., 6.]],
+                [[6., 6., 6.], [8., 8., 8.]]]
 
-def test_help_option(script_runner):
-    ret = script_runner.run('scil_fibertube_tracking.py', '--help')
-    assert ret.success
+    in_mask = os.path.join(SCILPY_HOME, 'tracking',
+                            'seeding_mask.nii.gz')
+    mask_img = nib.load(in_mask)
 
+    sft = StatefulTractogram(streamlines, mask_img, Space.VOX, Origin.NIFTI)
+    sft.data_per_streamline = {
+        "diameters": [0.002, 0.001]
+    }
 
-def test_execution_(script_runner, monkeypatch):
-    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
-    in_tractogram = os.path.join(SCILPY_HOME, 'tracking', 'local.trk')
-    in_diameters = 'diameters.txt'
-    diameters = [0.0012, 0.0024, 0.0018, 0.0043, 0.0017,
-                 0.0013, 0.0011, 0.0028, 0.0016, 0.0036] * 100
-    np.savetxt(in_diameters, diameters)
-    in_mask = os.path.join(SCILPY_HOME, 'tracking', 'seeding_mask.nii.gz')
+    save_tractogram(sft, 'tractogram.trk', True)
 
-    ret = script_runner.run('scil_fibertube_tracking.py',
-                            in_tractogram, in_diameters, in_mask,
-                            'tracking.trk', '1', '1', '--nb_seeds_per_fiber',
-                            '1', '--nb_fibers', '1', '-f')
 
+def test_help_option(script_runner):
+    ret = script_runner.run('scil_fibertube_tracking.py', '--help',
+                            '--min_length', '0')
     assert ret.success
 
 
-def test_execution_single_diameter(script_runner, monkeypatch):
+def test_execution(script_runner, monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
-    in_tractogram = os.path.join(SCILPY_HOME, 'tracking', 'local.trk')
-    in_diameters = 'diameters.txt'
-    diameters = [0.0025]
-    np.savetxt(in_diameters, diameters)
-    in_mask = os.path.join(SCILPY_HOME, 'tracking', 'seeding_mask.nii.gz')
-
+    init_data()
     ret = script_runner.run('scil_fibertube_tracking.py',
-                            in_tractogram, in_diameters, in_mask,
-                            'tracking.trk', '1', '1', '--nb_seeds_per_fiber',
-                            '1', '--nb_fibers', '1', '--single_diameter', '-f')
+                            'tractogram.trk', 'tracking.trk', '0.1', '0.3',
+                            '--min_length', '0', '-f')
 
     assert ret.success
 
 
-def test_execution_forward_only(script_runner, monkeypatch):
+def test_execution_tracking_rk(script_runner, monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
-    in_tractogram = os.path.join(SCILPY_HOME, 'tracking', 'local.trk')
-    in_diameters = 'diameters.txt'
-    diameters = [0.0012, 0.0024, 0.0018, 0.0043, 0.0017,
-                 0.0013, 0.0011, 0.0028, 0.0016, 0.0036] * 100
-    np.savetxt(in_diameters, diameters)
-    in_mask = os.path.join(SCILPY_HOME, 'tracking', 'seeding_mask.nii.gz')
-
+    init_data()
     ret = script_runner.run('scil_fibertube_tracking.py',
-                            in_tractogram, in_diameters, in_mask,
-                            'tracking.trk', '1', '1', '--nb_seeds_per_fiber',
-                            '1', '--nb_fibers', '1', '--forward_only', '-f')
+                            'tractogram.trk', 'tracking.trk', '0.1', '0.3',
+                            '--rk_order', '2', '--min_length', '0', '-f')
 
     assert ret.success
 
 
-def test_execution_no_compression(script_runner, monkeypatch):
+def test_execution_config(script_runner, monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
-    in_tractogram = os.path.join(SCILPY_HOME, 'tracking', 'local.trk')
-    in_diameters = 'diameters.txt'
-    diameters = [0.0012, 0.0024, 0.0018, 0.0043, 0.0017,
-                 0.0013, 0.0011, 0.0028, 0.0016, 0.0036] * 100
-    np.savetxt(in_diameters, diameters)
-    in_mask = os.path.join(SCILPY_HOME, 'tracking', 'seeding_mask.nii.gz')
-
+    init_data()
     ret = script_runner.run('scil_fibertube_tracking.py',
-                            in_tractogram, in_diameters, in_mask,
-                            'tracking.trk', '1', '1', '--nb_seeds_per_fiber',
-                            '1', '--nb_fibers', '1', '--do_not_compress', '-f')
+                            'tractogram.trk', 'tracking.trk', '0.1', '0.3',
+                            '--out_config', 'config.txt',
+                            '--min_length', '0', '-f')
 
     assert ret.success
 
 
-def test_execution_saving(script_runner, monkeypatch):
+def test_execution_seeding(script_runner, monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
-    in_tractogram = os.path.join(SCILPY_HOME, 'tracking', 'local.trk')
-    in_diameters = 'diameters.txt'
-    diameters = [0.0012, 0.0024, 0.0018, 0.0043, 0.0017,
-                 0.0013, 0.0011, 0.0028, 0.0016, 0.0036] * 100
-    np.savetxt(in_diameters, diameters)
-    in_mask = os.path.join(SCILPY_HOME, 'tracking', 'seeding_mask.nii.gz')
-
+    init_data()
     ret = script_runner.run('scil_fibertube_tracking.py',
-                            in_tractogram, in_diameters, in_mask,
-                            'tracking.trk', '1', '1', '--nb_seeds_per_fiber',
-                            '1', '--nb_fibers', '1', '--save_seeds',
-                            '--save_config', '-f')
+                            'tractogram.trk', 'tracking.trk', '0.1', '0.3',
+                            '--nb_fibers', '1', '--nb_seeds_per_fiber', '3',
+                            '--skip', '3', '--min_length', '0', '-f')
 
     assert ret.success
 
-
-def test_execution_shuffle(script_runner, monkeypatch):
-    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
-    in_tractogram = os.path.join(SCILPY_HOME, 'tracking', 'local.trk')
-    in_diameters = 'diameters.txt'
-    diameters = [0.0012, 0.0024, 0.0018, 0.0043, 0.0017,
-                 0.0013, 0.0011, 0.0028, 0.0016, 0.0036] * 100
-    np.savetxt(in_diameters, diameters)
-    in_mask = os.path.join(SCILPY_HOME, 'tracking', 'seeding_mask.nii.gz')
-
-    ret = script_runner.run('scil_fibertube_tracking.py',
-                            in_tractogram, in_diameters, in_mask,
-                            'tracking.trk', '1', '1', '--nb_seeds_per_fiber',
-                            '1', '--nb_fibers', '1', '--shuffle', '-f')
-
-    assert ret.success