arrayview 0.47.3__tar.gz → 0.47.4__tar.gz

{arrayview-0.47.3 → arrayview-0.47.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: arrayview
-Version: 0.47.3
+Version: 0.47.4
 Summary: Fast multi-dimensional array viewer
 Project-URL: Home, https://github.com/oscarvanderheide/arrayview
 Project-URL: Source, https://github.com/oscarvanderheide/arrayview

{arrayview-0.47.3 → arrayview-0.47.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "arrayview"
-version = "0.47.3"
+version = "0.47.4"
 description = "Fast multi-dimensional array viewer"
 readme = { file = "README.md", content-type = "text/markdown" }
 requires-python = ">=3.12"

{arrayview-0.47.3 → arrayview-0.47.4}/src/arrayview/_io.py

@@ -667,7 +667,7 @@ class _FileSeries:
     """Lazy 4D/5D view over a directory of same-shape array files.
 
     Like ``_NiftiSeries`` but works with any supported file format
-    (.npy, .npz, .zarr, .pt/.pth, .h5/.hdf5, .tif/.tiff, .mat).
+    (.npy, .npz, .zarr, .pt/.pth, .h5/.hdf5, .tif/.tiff, .mat, .gipl).
     Uses ``load_data`` for each volume — no nibabel reorientation.
     """
 
@@ -940,6 +940,8 @@ def _get_ext(filepath):
         return ".nii.gz"
     if lower.endswith(".zarr.zip"):
         return ".zarr.zip"
+    if lower.endswith(".gipl.gz"):
+        return ".gipl.gz"
     return os.path.splitext(lower)[1]
 
 
@@ -950,7 +952,7 @@ def _is_supported_collection_path(filepath):
 def _strip_array_ext(filepath):
     base = os.path.basename(filepath)
     lower = base.lower()
-    for suffix in (".nii.gz", ".zarr.zip"):
+    for suffix in (".nii.gz", ".zarr.zip", ".gipl.gz"):
         if lower.endswith(suffix):
             return base[: -len(suffix)]
     return os.path.splitext(base)[0]
@@ -1738,6 +1740,8 @@ def load_data(filepath, key=None, *, progress=None):
         import tifffile
 
         return tifffile.imread(filepath)
+    elif filepath.lower().endswith((".gipl", ".gipl.gz")):
+        return _load_gipl(filepath)
     elif filepath.endswith(".mat"):
         try:
             import scipy.io
@@ -1783,10 +1787,68 @@ def load_data(filepath, key=None, *, progress=None):
             return data
         raise ValueError(
             "Unsupported format. Supported: .npy, .npz, .nii/.nii.gz, .zarr, "
-            ".pt/.pth, .h5/.hdf5, .tif/.tiff, .mat"
+            ".pt/.pth, .h5/.hdf5, .tif/.tiff, .mat, .gipl/.gipl.gz"
         )
 
 
+# GIPL (Guys Image Processing Lab) image types -> numpy dtypes. Data is
+# big-endian; complex types store interleaved real/imaginary components.
+_GIPL_DTYPES = {
+    1: ">u1",  # binary, one value per byte
+    7: ">i1",
+    8: ">u1",
+    15: ">i2",
+    16: ">u2",
+    31: ">u4",
+    32: ">i4",
+    64: ">f4",
+    65: ">f8",
+    144: ">i2",  # complex short
+    160: ">i4",  # complex int
+    192: ">f4",  # complex float
+    193: ">f8",  # complex double
+}
+_GIPL_COMPLEX = frozenset([144, 160, 192, 193])
+_GIPL_MAGIC = (4026526128, 719555000)
+_GIPL_HEADER_SIZE = 256
+
+
+def _load_gipl(filepath):
+    """Read a .gipl/.gipl.gz file into an array indexed (x, y, z, t).
+
+    Trailing singleton dimensions are dropped, matching how a NIfTI volume
+    of the same data is shown.
+    """
+    import gzip
+
+    opener = gzip.open if filepath.lower().endswith(".gz") else open
+    with opener(filepath, "rb") as f:
+        raw = f.read()
+    if len(raw) < _GIPL_HEADER_SIZE:
+        raise ValueError(f"{filepath!r} is too short to be a GIPL file.")
+    header = raw[:_GIPL_HEADER_SIZE]
+    magic = int(np.frombuffer(header, ">u4", count=1, offset=252)[0])
+    if magic not in _GIPL_MAGIC:
+        raise ValueError(f"{filepath!r} is not a GIPL file (bad magic number).")
+    dims = [int(d) for d in np.frombuffer(header, ">u2", count=4, offset=0)]
+    image_type = int(np.frombuffer(header, ">u2", count=1, offset=8)[0])
+    if image_type not in _GIPL_DTYPES:
+        raise ValueError(f"{filepath!r} has unsupported GIPL image type {image_type}.")
+    dims = [max(d, 1) for d in dims]
+    is_complex = image_type in _GIPL_COMPLEX
+    count = int(np.prod(dims)) * (2 if is_complex else 1)
+    data = np.frombuffer(raw, _GIPL_DTYPES[image_type], count=count, offset=_GIPL_HEADER_SIZE)
+    data = data.astype(data.dtype.newbyteorder("="))
+    if is_complex:
+        data = data.astype(np.float64 if data.itemsize == 8 else np.float32)
+        data = data[0::2] + 1j * data[1::2]
+    # x varies fastest on disk.
+    arr = data.reshape(dims[::-1]).transpose(3, 2, 1, 0)
+    while arr.ndim > 2 and arr.shape[-1] == 1:
+        arr = arr[..., 0]
+    return np.ascontiguousarray(arr)
+
+
 def _tensor_to_numpy(obj, source="object"):
     """Convert a tensor-like object (PyTorch, etc.) to a numpy array."""
     if isinstance(obj, np.ndarray):
@@ -1823,13 +1885,15 @@ _SUPPORTED_EXTS = frozenset(
         ".tif",
         ".tiff",
         ".mat",
+        ".gipl",
+        ".gipl.gz",
         ".dcm",
     ]
 )
 
 # Formats that load the entire array into RAM (no mmap/lazy access).
 # RAM guard only applies to these.
-FULL_LOAD_EXTS = frozenset([".pt", ".pth", ".tif", ".tiff", ".mat"])
+FULL_LOAD_EXTS = frozenset([".pt", ".pth", ".tif", ".tiff", ".mat", ".gipl", ".gipl.gz"])
 
 
 def _peek_file_shape(fpath: str, ext: str):

{arrayview-0.47.3 → arrayview-0.47.4}/src/arrayview/_launcher.py

@@ -6211,17 +6211,18 @@ def arrayview():
             pattern for _name, pattern in _normalize_dir_overlay_specs(args.overlay or [])
         )
         collection_inputs.extend(args.overlay_dir or [])
-        for pattern in collection_inputs:
-            pattern = lexical_abspath(pattern)
-            probe_prefix = scan_root_before_magic(pattern)
-            mount = direct_network_mount(probe_prefix)
-            nested_mount = network_mount_below(probe_prefix)
-            if mount is not None or nested_mount is not None:
-                _print_failure(
-                    "network directory collections are not accessed directly. "
-                    "Copy the collection to local storage before using --match."
-                )
-                sys.exit(1)
+        if os.environ.get("ARRAYVIEW_SKIP_SOURCE_STAGING", "1") == "0":
+            for pattern in collection_inputs:
+                pattern = lexical_abspath(pattern)
+                probe_prefix = scan_root_before_magic(pattern)
+                mount = direct_network_mount(probe_prefix)
+                nested_mount = network_mount_below(probe_prefix)
+                if mount is not None or nested_mount is not None:
+                    _print_failure(
+                        "network directory collections are not accessed directly. "
+                        "Copy the collection to local storage before using --match."
+                    )
+                    sys.exit(1)
         if len(dir_patterns) == 1 and os.path.isdir(dir_patterns[0]):
             dir_patterns = [os.path.join(dir_patterns[0], "**", "*")]
         dir_overlay_specs = [

{arrayview-0.47.3 → arrayview-0.47.4}/src/arrayview/_routes_loading.py

@@ -167,17 +167,17 @@ def register_loading_routes(app, *, notify_shells, setup_rgb) -> None:
                             f"{nested_sibling_mount.mountpoint!r}; copy the series locally first."
                         )
                     }
-        for pattern in dir_patterns or []:
-            pattern_path = lexical_abspath(str(pattern))
-            scan_root = scan_root_before_magic(pattern_path)
-            unsafe_mount = direct_network_mount(scan_root) or network_mount_below(scan_root)
-            if unsafe_mount is not None:
-                return {
-                    "error": (
-                        f"Directory scan would enter network mount "
-                        f"{unsafe_mount.mountpoint!r}; copy the collection locally first."
-                    )
-                }
+            for pattern in dir_patterns or []:
+                pattern_path = lexical_abspath(str(pattern))
+                scan_root = scan_root_before_magic(pattern_path)
+                unsafe_mount = direct_network_mount(scan_root) or network_mount_below(scan_root)
+                if unsafe_mount is not None:
+                    return {
+                        "error": (
+                            f"Directory scan would enter network mount "
+                            f"{unsafe_mount.mountpoint!r}; copy the collection locally first."
+                        )
+                    }
         if requested_sid in CANCELLED_PENDING_SESSIONS:
             CANCELLED_PENDING_SESSIONS.discard(requested_sid)
             raise HTTPException(status_code=409, detail="load request was cancelled")

{arrayview-0.47.3 → arrayview-0.47.4}/src/arrayview/_source_safety.py

@@ -53,6 +53,8 @@ _KNOWN_LOCAL_STAGE_FILESYSTEMS = frozenset(
     }
 )
 _SELF_CONTAINED_FILE_EXTENSIONS = (
+    ".gipl",
+    ".gipl.gz",
     ".h5",
     ".hdf5",
     ".mat",

{arrayview-0.47.3 → arrayview-0.47.4}/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 = "0.15.63"  # current bundled extension version
+_VSCODE_EXT_VERSION = "0.15.64"  # 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-0.47.3 → arrayview-0.47.4}/tests/test_api.py

@@ -423,6 +423,30 @@ class TestLoad:
         assert "Direct server access" in response.json()["error"]
         assert time.monotonic() - started < 2
 
+    @pytest.mark.parametrize("staging", [None, "1", "0"])
+    @pytest.mark.parametrize("nested", [False, True])
+    def test_network_collection_respects_staging_setting(self, client, tmp_path, monkeypatch, staging, nested):
+        images = tmp_path / "images"
+        images.mkdir()
+        np.save(images / "case_a.npy", np.ones((4, 5, 6), dtype=np.float32))
+        mountpoint = images if nested else tmp_path
+        mountinfo = tmp_path / "mountinfo"
+        mountinfo.write_text(f"42 31 0:55 / {mountpoint} rw - cifs //server/share rw\n")
+        monkeypatch.setenv("_ARRAYVIEW_TEST_MOUNTINFO", str(mountinfo))
+        if staging is None:
+            monkeypatch.delenv("ARRAYVIEW_SKIP_SOURCE_STAGING", raising=False)
+        else:
+            monkeypatch.setenv("ARRAYVIEW_SKIP_SOURCE_STAGING", staging)
+        pattern = str(tmp_path / "*" / "case_a.npy") if nested else str(images / "*.npy")
+        body = client.post("/load", json={"dir_patterns": [pattern]}).json()
+        if staging == "0":
+            assert "network mount" in body["error"]
+        else:
+            assert "error" not in body
+            meta = client.get(f"/metadata/{body['sid']}").json()
+            assert meta["shape"] == [4, 5, 6, 1]
+            assert meta["case_names"] == ["case_a"]
+
     def test_load_rejects_arbitrary_staging_cleanup_authority(
         self, client, arr_2d, tmp_path, monkeypatch
     ):

{arrayview-0.47.3 → arrayview-0.47.4}/tests/test_cli.py

@@ -477,6 +477,34 @@ def test_cli_dir_dry_run_prints_collection_summary(monkeypatch, tmp_path):
     assert "caseA, caseB" in text
 
 
+@pytest.mark.parametrize("staging", [None, "1", "0"])
+@pytest.mark.parametrize("nested", [False, True])
+def test_cli_network_collection_respects_staging_setting(monkeypatch, tmp_path, staging, nested):
+    images = tmp_path / "images"
+    images.mkdir()
+    np.save(images / "case_a.npy", np.ones((4, 5, 6), dtype=np.float32))
+    mountpoint = images if nested else tmp_path
+    mountinfo = tmp_path / "mountinfo"
+    mountinfo.write_text(f"42 31 0:55 / {mountpoint} rw - cifs //server/share rw\n")
+    monkeypatch.setenv("_ARRAYVIEW_TEST_MOUNTINFO", str(mountinfo))
+    if staging is None:
+        monkeypatch.delenv("ARRAYVIEW_SKIP_SOURCE_STAGING", raising=False)
+    else:
+        monkeypatch.setenv("ARRAYVIEW_SKIP_SOURCE_STAGING", staging)
+    pattern = str(tmp_path / "*" / "case_a.npy") if nested else str(images / "*.npy")
+    monkeypatch.setattr(sys, "argv", ["arrayview", "--match", pattern, "--dry-run"])
+    stdout = io.StringIO()
+    monkeypatch.setattr(sys, "stdout", stdout)
+    if staging == "0":
+        with pytest.raises(SystemExit) as exc:
+            appmod.arrayview()
+        assert exc.value.code == 1
+        assert "network directory collections" in stdout.getvalue()
+    else:
+        appmod.arrayview()
+        assert "cases: 1" in stdout.getvalue()
+
+
 def test_cli_stack_can_continue_with_only_cases_that_have_overlays(
     monkeypatch, tmp_path
 ):

{arrayview-0.47.3 → arrayview-0.47.4}/tests/test_io.py

@@ -51,3 +51,41 @@ def test_mat_loader_returns_key_list_for_multiple_numeric_arrays(tmp_path):
         np.ones((4, 5), dtype=np.uint16),
     )
 
+
+
+def _write_gipl(path, xyz, image_type, opener=open):
+    header = bytearray(256)
+    dims = list(xyz.shape) + [1] * (4 - xyz.ndim)
+    header[0:8] = np.array(dims, ">u2").tobytes()
+    header[8:10] = np.array([image_type], ">u2").tobytes()
+    header[252:256] = np.array([4026526128], ">u4").tobytes()
+    with opener(path, "wb") as f:
+        f.write(bytes(header) + xyz.T.astype(xyz.dtype.newbyteorder(">")).tobytes())
+
+
+def test_gipl_loader_reads_x_y_z_order_plain_and_gzipped(tmp_path):
+    import gzip
+
+    from arrayview._io import _SUPPORTED_EXTS, _get_ext, load_data
+
+    expected = np.arange(4 * 5 * 3, dtype=np.int16).reshape(4, 5, 3) - 30
+    _write_gipl(tmp_path / "vol.gipl", expected, 15)
+    _write_gipl(tmp_path / "vol.gipl.gz", expected, 15, opener=gzip.open)
+
+    for name in ("vol.gipl", "vol.gipl.gz"):
+        path = str(tmp_path / name)
+        assert _get_ext(path) in _SUPPORTED_EXTS
+        loaded = load_data(path)
+        assert loaded.dtype == np.int16
+        np.testing.assert_array_equal(loaded, expected)
+
+
+def test_gipl_loader_rejects_non_gipl_file(tmp_path):
+    import pytest
+
+    from arrayview._io import load_data
+
+    path = tmp_path / "bogus.gipl"
+    path.write_bytes(bytes(300))
+    with pytest.raises(ValueError, match="not a GIPL file"):
+        load_data(str(path))