arrayview 0.47.0__tar.gz → 0.47.1__tar.gz

{arrayview-0.47.0 → arrayview-0.47.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: arrayview
-Version: 0.47.0
+Version: 0.47.1
 Summary: Fast multi-dimensional array viewer
 Project-URL: Home, https://github.com/oscarvanderheide/arrayview
 Project-URL: Source, https://github.com/oscarvanderheide/arrayview

{arrayview-0.47.0 → arrayview-0.47.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "arrayview"
-version = "0.47.0"
+version = "0.47.1"
 description = "Fast multi-dimensional array viewer"
 readme = { file = "README.md", content-type = "text/markdown" }
 requires-python = ">=3.12"

{arrayview-0.47.0 → arrayview-0.47.1}/src/arrayview/_io.py

@@ -1863,3 +1863,44 @@ def _peek_file_shape(fpath: str, ext: str):
     except Exception:
         pass
     return None
+
+
+def nifti_grid_meta(filepath):
+    """Return a NIfTI file's native-order spatial metadata (header only), or None."""
+    if not (filepath.endswith(".nii") or filepath.endswith(".nii.gz")):
+        return None
+    return _nifti_header_with_meta(filepath, native=True)[1]
+
+
+def align_overlay_to_base(ov_path, ov_data, base_meta):
+    """Resample a NIfTI overlay onto the base volume's voxel grid.
+
+    Only used when the overlay's spatial shape differs from the base, which
+    otherwise leaves the overlay undisplayable. Both files' affines place the
+    voxels in world space; label data uses nearest-neighbour so mask values
+    stay exact. Returns ``ov_data`` unchanged when alignment does not apply.
+    """
+    if not base_meta or not (ov_path.endswith(".nii") or ov_path.endswith(".nii.gz")):
+        return ov_data
+    base_shape = base_meta.get("spatial_shape")
+    base_affine = base_meta.get("data_affine")
+    if base_shape is None or base_affine is None:
+        return ov_data
+    ov_shape = tuple(int(v) for v in ov_data.shape)
+    if len(ov_shape) != 3 or ov_shape == tuple(base_shape):
+        return ov_data
+    from scipy.ndimage import affine_transform
+
+    ov_affine = np.asarray(_nib().load(ov_path).affine, dtype=np.float64)
+    base_to_ov = np.linalg.inv(ov_affine) @ np.asarray(base_affine, dtype=np.float64)
+    src = np.asarray(ov_data)
+    is_label = np.issubdtype(src.dtype, np.integer) or src.dtype == bool
+    return affine_transform(
+        src.astype(np.float32) if not is_label else src,
+        base_to_ov[:3, :3],
+        offset=base_to_ov[:3, 3],
+        output_shape=tuple(base_shape),
+        order=0 if is_label else 1,
+        mode="constant",
+        cval=0,
+    )

{arrayview-0.47.0 → arrayview-0.47.1}/src/arrayview/_launcher.py

@@ -1314,6 +1314,7 @@ def _load_session_from_filepath(
     watch: bool = False,
     initial_view: dict | None = None,
     code_source: dict | None = None,
+    align_to: str | None = None,
 ) -> dict:
     requested_sid = uuid.uuid4().hex
     payload = {
@@ -1329,6 +1330,8 @@ def _load_session_from_filepath(
     }
     if source_staging_dir:
         payload["source_staging_dir"] = source_staging_dir
+    if align_to:
+        payload["align_to"] = align_to
     if watch:
         payload["watch"] = True
     if initial_view:
@@ -1686,6 +1689,7 @@ def _register_cli_session_with_existing_server_impl(
             ov_name,
             expected_server_id=expected_server_id,
             source_staging_dir=(source_staging_dirs or {}).get(ov_path),
+            align_to=os.path.abspath(base_file),
         )
         if "error" in ov_result:
             raise RuntimeError(
@@ -4803,6 +4807,7 @@ def _serve_daemon(
             array_choice_placeholder,
             load_data,
             load_data_with_meta,
+            align_overlay_to_base,
             load_dir_collection,
             list_array_keys,
         )
@@ -4928,6 +4933,7 @@ def _serve_daemon(
             ):
                 try:
                     ov_data = load_data(ov_path)
+                    ov_data = align_overlay_to_base(ov_path, ov_data, spatial_meta)
                     ov_session = _session_mod.Session(
                         ov_data, filepath=ov_path, name=ov_name
                     )

{arrayview-0.47.0 → arrayview-0.47.1}/src/arrayview/_routes_loading.py

@@ -277,6 +277,7 @@ def register_loading_routes(app, *, notify_shells, setup_rgb) -> None:
                     and os.path.abspath(existing.filepath) == abs_path
                     and current_signature is not None
                     and getattr(existing, "file_signature", None) == current_signature
+                    and getattr(existing, "aligned_to", None) == body.get("align_to")
                 ):
                     if acquire_session_leases([existing.sid]):
                         return {"sid": existing.sid, "name": existing.name, "notified": False}
@@ -458,6 +459,17 @@ def register_loading_routes(app, *, notify_shells, setup_rgb) -> None:
                         key=_key,
                         select=body.get("select"),
                     )
+                    if body.get("align_to"):
+                        from ._io import align_overlay_to_base, nifti_grid_meta
+
+                        base_meta = await asyncio.to_thread(
+                            nifti_grid_meta, str(body["align_to"])
+                        )
+                        aligned = await asyncio.to_thread(
+                            align_overlay_to_base, filepath, data, base_meta
+                        )
+                        if aligned is not data:
+                            data, spatial_meta = aligned, base_meta
             except Exception as e:
                 if staging_dir:
                     cleanup_staging_directory(staging_dir)
@@ -479,6 +491,7 @@ def register_loading_routes(app, *, notify_shells, setup_rgb) -> None:
                 str(value) for value in body.get("related_sids", [])
             ]
             apply_launch_view(session, body)
+            session.aligned_to = body.get("align_to")
             if staging_dir:
                 session._source_staging_dirs = [str(staging_dir)]
             if not dir_patterns:

{arrayview-0.47.0 → arrayview-0.47.1}/src/arrayview/_session.py

@@ -765,6 +765,12 @@ def upgrade_memmap_in_background(session) -> bool:
                 from ._io import _nifti_display_array
 
                 loaded = _nifti_display_array(data)
+                # An uncompressed proxy whose dtype needs no conversion comes
+                # back as a view of the file map, so nothing was read yet and
+                # every new orientation would still fault from disk. Copy in
+                # file order to make it one sequential read.
+                if not loaded.flags.owndata:
+                    loaded = np.array(loaded, copy=True, order="K")
         except Exception:
             return  # keep serving from the lazy source
         # A /reload or a released session must not be clobbered by a read that

{arrayview-0.47.0 → arrayview-0.47.1}/tests/test_api.py

@@ -7844,3 +7844,23 @@ class TestViewDisplayRouting:
         finally:
             for sid in set(session_mod.SESSIONS) - before_sids:
                 session_mod.SESSIONS.pop(sid, None)
+
+
+def test_load_aligns_nifti_overlay_to_requested_base_grid(client, tmp_path):
+    nib = pytest.importorskip("nibabel")
+    import arrayview._session as session_mod
+
+    affine = np.diag([1.0, 1.0, 2.0, 1.0])
+    base = tmp_path / "base.nii.gz"
+    nib.save(nib.Nifti1Image(np.zeros((6, 6, 5), np.float32), affine), str(base))
+    mask = tmp_path / "mask.nii.gz"
+    nib.save(nib.Nifti1Image(np.ones((6, 6, 4), np.uint8), affine), str(mask))
+
+    plain = client.post("/load", json={"filepath": str(mask)}).json()["sid"]
+    aligned = client.post(
+        "/load", json={"filepath": str(mask), "align_to": str(base)}
+    ).json()["sid"]
+
+    assert aligned != plain
+    assert session_mod.SESSIONS[plain].shape == (6, 6, 4)
+    assert session_mod.SESSIONS[aligned].shape == (6, 6, 5)

{arrayview-0.47.0 → arrayview-0.47.1}/tests/test_nifti_meta.py

@@ -172,3 +172,26 @@ def test_explicit_ras_conversion_reorients_native_volume(client, tmp_path):
     reverted = client.post(f"/resample_ras/{sid}", json={"enabled": False})
     reverted.raise_for_status()
     assert reverted.json()["shape"] == [3, 4, 5]
+
+
+def test_overlay_on_different_grid_is_resampled_onto_base(tmp_path):
+    from arrayview._io import align_overlay_to_base, load_data, load_data_with_meta
+
+    base_affine = np.diag([1.0, 1.0, 2.0, 1.0])
+    nib.save(nib.Nifti1Image(np.zeros((8, 8, 6), np.float32), base_affine), tmp_path / "base.nii.gz")
+    # Mask has one slice fewer and starts one base slice (2 mm) higher.
+    mask = np.zeros((8, 8, 5), np.uint8)
+    mask[2:4, 3:5, 1] = 1
+    mask_affine = base_affine.copy()
+    mask_affine[2, 3] = 2.0
+    nib.save(nib.Nifti1Image(mask, mask_affine), tmp_path / "mask.nii.gz")
+
+    _base, meta = load_data_with_meta(str(tmp_path / "base.nii.gz"))
+    path = str(tmp_path / "mask.nii.gz")
+    aligned = align_overlay_to_base(path, load_data(path), meta)
+
+    assert aligned.shape == (8, 8, 6)
+    assert aligned.dtype == np.uint8
+    expected = np.zeros((8, 8, 6), np.uint8)
+    expected[2:4, 3:5, 2] = 1
+    np.testing.assert_array_equal(aligned, expected)