arrayview 0.47.0__tar.gz → 0.47.3__tar.gz

{arrayview-0.47.0 → arrayview-0.47.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: arrayview
-Version: 0.47.0
+Version: 0.47.3
 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-0.47.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "arrayview"
-version = "0.47.0"
+version = "0.47.3"
 description = "Fast multi-dimensional array viewer"
 readme = { file = "README.md", content-type = "text/markdown" }
 requires-python = ">=3.12"

{arrayview-0.47.0 → arrayview-0.47.3}/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-0.47.3}/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-0.47.3}/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-0.47.3}/src/arrayview/_routes_preferences.py

@@ -37,7 +37,7 @@ def _response_payload() -> dict:
     if not native_available:
         defaults["window"]["default"] = "browser"
         defaults["window"]["terminal"] = "browser"
-        for key in ("default", "terminal", "vscode", "jupyter", "julia"):
+        for key in ("terminal", "vscode", "jupyter", "julia"):
             schema["window"][key] = [
                 value for value in schema["window"][key] if value != "native"
             ]

{arrayview-0.47.0 → arrayview-0.47.3}/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-0.47.3}/src/arrayview/_viewer.html

@@ -7086,6 +7086,7 @@
         let _mvPrevZoom = 1.0;
         let _cmvPrevSquareStretch = false;
         let _qmriPrevZoom = 1.0;  // saved on enterQmri, restored on exitQmri (mirrors _mvPrevZoom)
+        let _qmriPrevActiveDim = null;  // scroll dim before qMRI moved it off the map dim; null while rebuilding keeps the original
         let _comparePrevZoom = 1.0;  // saved on enterCompareMode, restored on exitCompareMode
         let _comparePrevNormalView = null; // Phase 4: saved primary View, restored on exitCompareMode
         let _eggsVisible = true;
@@ -35472,6 +35473,7 @@
             if (multiViewActive) exitMultiView();
             if (stackMosaicActive) exitStackMosaic();
             _qmriPrevZoom = userZoom;  // save prior zoom so exitQmri can restore (mirrors enterMultiView)
+            if (_qmriPrevActiveDim === null) _qmriPrevActiveDim = activeDim;
             userZoom = 1.0;
             qvPan.reset();
             // Opening straight into qMRI never draws the main canvas, so its
@@ -35994,6 +35996,10 @@
             wrap.innerHTML = '';
             wrap.className = '';
             userZoom = _qmriPrevZoom;  // restore prior zoom (mirrors exitMultiView line 10521)
+            if (!_qmriSyntheticRebuilding && _qmriPrevActiveDim !== null) {
+                if (_qmriPrevActiveDim < shape.length) activeDim = _qmriPrevActiveDim;
+                _qmriPrevActiveDim = null;
+            }
             if (!_qmriSyntheticRebuilding) updateView();
             _reconcileUI();
             renderInfo();

{arrayview-0.47.0 → arrayview-0.47.3}/src/arrayview/_vscode_extension.py

@@ -58,7 +58,7 @@ _VSCODE_EXT_FRESH_INSTALL = False  # True if we just installed it this session
 _VSCODE_EXT_RELOAD_REQUIRED = False  # installed files are newer than the live host
 _VSCODE_EXT_INSTALL_FAILED = False  # automatic install could not complete safely
 _VSCODE_EXT_NO_LIVE_WINDOW = False  # no live host claims this terminal's window id
-_VSCODE_EXT_VERSION = "0.15.62"  # current bundled extension version
+_VSCODE_EXT_VERSION = "0.15.63"  # current bundled extension version
 _VSCODE_CONFIGURED_PORTS: set[int] = set()
 # Version-skew notices already printed, so a long-lived process (Jupyter, a
 # script opening several arrays) states the mismatch once instead of per call.

{arrayview-0.47.0 → arrayview-0.47.3}/tests/conftest.py

@@ -34,6 +34,21 @@ def isolated_runtime_directory(tmp_path_factory, monkeypatch):
     )
 
 
+@pytest.fixture(autouse=True)
+def no_leaked_fake_sessions():
+    """Drop anything a test put in the shared session table that isn't a session.
+
+    The test server is shared by the whole run, so one stray placeholder makes
+    every later load in every later file fail.
+    """
+    from arrayview._session import SESSIONS, Session
+
+    yield
+    for sid, value in list(SESSIONS.items()):
+        if not isinstance(value, Session):
+            SESSIONS.pop(sid, None)
+
+
 # ---------------------------------------------------------------------------
 # Server
 # ---------------------------------------------------------------------------