fix tests after bug fixes in scan RAS conversion

mne-tools · Dec 6, 2023 · 5e3804d · 5e3804d
1 parent dfdc492
commit 5e3804d
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Showing 2 changed files with 18 additions and 45 deletions.
diff --git a/mne_gui_addons/_ieeg_locate.py b/mne_gui_addons/_ieeg_locate.py
@@ -966,13 +966,13 @@ def mark_channel(self, ch=None):
             self._chs[name][:] = self._ras
         else:
             neighbors = _voxel_neighbors(
-                self._vox,
+                apply_trans(self._scan_ras_ras_vox_t, self._ras),
                 self._ct_data,
                 thresh=_VOXEL_NEIGHBORS_THRESH,
                 voxels_max=self._radius**3,
                 use_relative=True,
             )
-            self._chs[name][:] = apply_trans(  # to surface RAS
+            self._chs[name][:] = apply_trans(
                 self._ras_vox_scan_ras_t, np.array(list(neighbors)).mean(axis=0)
             )
         self._color_list_item()

diff --git a/mne_gui_addons/tests/test_ieeg_locate.py b/mne_gui_addons/tests/test_ieeg_locate.py
@@ -61,7 +61,7 @@ def _fake_CT_coords(skull_size=5, contact_size=2):
             np.array(np.meshgrid(*[range(-contact_size, contact_size + 1)] * 3)), axis=0
         )
     ct = nib.MGHImage(ct_data, brain.affine)
-    coords = apply_trans(ct.header.get_vox2ras_tkr(), np.array(coords))
+    coords = apply_trans(ct.header.get_vox2ras(), np.array(coords))
     return ct, coords
 
 
@@ -157,17 +157,15 @@ def test_ieeg_elec_locate_display(renderer_interactive_pyvistaqt, _fake_CT_coord
         gui._ras[:] = coords[0]
 
     # start in the right position
-    gui.set_RAS(apply_trans(gui._mri_scan_ras_t, coords[0]))
+    gui.set_RAS(coords[0])
     gui.mark_channel()
 
     with pytest.raises(ValueError, match="not found"):
         gui.mark_channel("foo")
 
     assert not gui._lines and not gui._lines_2D  # no lines for one contact
     for ci, coord in enumerate(coords[1:], 1):
-        coord_vox = apply_trans(
-            gui._scan_ras_ras_vox_t, apply_trans(gui._mri_scan_ras_t, coord)
-        )
+        coord_vox = apply_trans(gui._scan_ras_ras_vox_t, coord)
         with use_log_level("debug"):
             _fake_click(
                 gui._figs[2],
@@ -177,13 +175,13 @@ def test_ieeg_elec_locate_display(renderer_interactive_pyvistaqt, _fake_CT_coord
                 kind="release",
             )
         assert_allclose(
-            apply_trans(gui._mri_scan_ras_t, coord)[:2],
+            coord[:2],
             gui._ras[:2],
             atol=0.1,
             err_msg=f"coords[{ci}][:2]",
         )
         assert_allclose(
-            apply_trans(gui._mri_scan_ras_t, coord)[2],
+            coord[2],
             gui._ras[2],
             atol=2,
             err_msg=f"coords[{ci}][2]",
@@ -195,29 +193,16 @@ def test_ieeg_elec_locate_display(renderer_interactive_pyvistaqt, _fake_CT_coord
 
     # test snap to center
     gui._ch_index = 0
-    gui.set_RAS(apply_trans(gui._mri_scan_ras_t, coords[0]))  # move to first position
+    gui.set_RAS(coords[0])  # move to first position
     gui.mark_channel()
-    assert (
-        abs(
-            np.linalg.norm(
-                apply_trans(gui._mri_scan_ras_t, coords[0]) - gui._chs["LAMY 1"]
-            )
-            - 1.03
-        )
-        < 1e-3
-    )
+    assert 0 < np.linalg.norm(coords[0] - gui._chs["LAMY 1"]) < 1
     gui._snap_button.click()
     assert gui._snap_button.text() == "Off"
     # now make sure no snap happens
     gui._ch_index = 0
-    gui.set_RAS(apply_trans(gui._mri_scan_ras_t, coords[1] + 1))
+    gui.set_RAS(coords[1] + 1)
     gui.mark_channel()
-    assert (
-        np.linalg.norm(
-            apply_trans(gui._mri_scan_ras_t, coords[1] + 1) - gui._chs["LAMY 1"]
-        )
-        < 1e-3
-    )
+    assert np.linalg.norm(coords[1] + 1 - gui._chs["LAMY 1"]) < 1e-3
     # check that it turns back on
     gui._snap_button.click()
     assert gui._snap_button.text() == "On"
@@ -259,40 +244,28 @@ def test_ieeg_elec_locate_display(renderer_interactive_pyvistaqt, _fake_CT_coord
     assert montage is not None
     assert_allclose(
         montage.get_positions()["ch_pos"]["LAMY 1"],
-        [5.276672, -9.030582, 27.302032],
+        [0.007262, 0.017135, 0.041672],
         atol=0.01,
     )
 
     # check auto find targets
     gui.remove_channel("LAMY 1")
     target, entry = (
-        apply_trans(gui._mri_scan_ras_t, coords[0]) / 1000,
-        apply_trans(gui._mri_scan_ras_t, coords[1]) / 1000,
+        coords[0] / 1000,
+        coords[1] / 1000,
     )
 
     # test just target
     gui.auto_find_contacts(targets={"LAMY ": target})
-    assert (
-        np.linalg.norm(apply_trans(gui._mri_scan_ras_t, coords[0]) - gui._chs["LAMY 1"])
-        < 1e-3
-    )
-    assert (
-        np.linalg.norm(apply_trans(gui._mri_scan_ras_t, coords[1]) - gui._chs["LAMY 2"])
-        < 1e-3
-    )
+    assert np.linalg.norm(coords[0] - gui._chs["LAMY 1"]) < 1e-3
+    assert np.linalg.norm(coords[1] - gui._chs["LAMY 2"]) < 1e-3
 
     gui.remove_channel("LAMY 1")
     gui.remove_channel("LAMY 2")
 
     # test with target and entry
     gui.auto_find_contacts(targets={"LAMY ": (target, entry)})
-    assert (
-        np.linalg.norm(apply_trans(gui._mri_scan_ras_t, coords[0]) - gui._chs["LAMY 1"])
-        < 1e-3
-    )
-    assert (
-        np.linalg.norm(apply_trans(gui._mri_scan_ras_t, coords[1]) - gui._chs["LAMY 2"])
-        < 1e-3
-    )
+    assert np.linalg.norm(coords[0] - gui._chs["LAMY 1"]) < 1e-3
+    assert np.linalg.norm(coords[1] - gui._chs["LAMY 2"]) < 1e-3
 
     gui.close()