arrayview 0.47.3__py3-none-any.whl → 0.47.4__py3-none-any.whl

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/_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/_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/_source_safety.py

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

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.dist-info → arrayview-0.47.4.dist-info}/METADATA

@@ -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.dist-info → arrayview-0.47.4.dist-info}/RECORD

@@ -12,10 +12,10 @@ arrayview/_extra_ports.py,sha256=MZcx04NI9Eg4coydb-yPIHp7uJbE6UscyYGnw8fxid0,111
 arrayview/_icon.png,sha256=a8RTAbvweLhh3hzD5eGg76Peq-KSDcS6YrCphRb_HEs,2748
 arrayview/_imaging.py,sha256=MQX1uy4m1lofOeoLDhCp6cHO5p_V5fXm4qlSu9Ykn-c,534
 arrayview/_instance_registry.py,sha256=h7vyvCl0LTt9R8sDB1Vxe4a-KzfkLVuwrSw_ANpPTD8,8833
-arrayview/_io.py,sha256=0QAKjU9WkBdXAfIAGv7HCeWpAwbn9TMCYlip36I2U4I,75238
+arrayview/_io.py,sha256=u1wrxfEA3kRT9n6tV-7ptcQxr1mOylZaREYq3Ex6nvM,77652
 arrayview/_launch_plan.py,sha256=KGgIPGsflXArECB2txnIAewjuPvF4fZTbO63alC8x28,23570
 arrayview/_launch_trace.py,sha256=4yjJdkFyEvSrPN14QVFJ3u6on2q0TH2ySSdgUp9SjKI,5668
-arrayview/_launcher.py,sha256=W_CjLFa3_D7IwTYmBX0-7h6XrX4EKvwsJqgbgIu8y7g,243108
+arrayview/_launcher.py,sha256=Eu1XFLhuXiO45StFWZoSPPjFkBLqcEeqGB8Utx7kotQ,243224
 arrayview/_lifecycle.py,sha256=bqG0oKr-e-5S1ssCTlGmF-yBE47ilrpO1S_Owfjs9Z8,5365
 arrayview/_overlays.py,sha256=CksypG9rWfCz_3RRGIeyaKeXse17AFxvkEjmYyXnIIE,5399
 arrayview/_platform.py,sha256=qSWjRcx9rLIdLvKrRArSueFnbyn5GPKfTEMOc5mCIUs,29970
@@ -23,7 +23,7 @@ arrayview/_render.py,sha256=sSNPWreJumIyFKvZtAS5v2gxbNHRVyAdc7JGj34caPw,34121
 arrayview/_routes_analysis.py,sha256=Xz9Ysr04u07pzSRB4Fzmcl6XwVxyaG6xCWxGwYZi_80,33085
 arrayview/_routes_drop.py,sha256=FC4e7STdCo3hYIA0C4Yy9Ka2UKFx7nLDU5dkujmc1Vo,12477
 arrayview/_routes_export.py,sha256=Ha8mMO2E9TlRL5x25-ADV8_8xUiC-jRz9N1oWwgKOsg,3898
-arrayview/_routes_loading.py,sha256=rC0cw4QRaTycvzvWemencUQCkCGyaT7GzUd9gH9Rc5Y,42360
+arrayview/_routes_loading.py,sha256=r88PRn1ogSRe1Ec0odhCN3jd5FwIDH0y7acPdUoY9v0,42404
 arrayview/_routes_persistence.py,sha256=T03csHb7ppGT-8yMDf227XkqhnhjgSLYj0RW2wmg59g,17176
 arrayview/_routes_preferences.py,sha256=xoMHbPKliYspgjaclhx2r8HbP9mFo9Td-nTF76eWVMg,4680
 arrayview/_routes_preload.py,sha256=KOsankNguxdIWmFW9iZcY9p2SvUN1mOKY7KkW1qMGcc,1729
@@ -38,7 +38,7 @@ arrayview/_server.py,sha256=A8O8J6N4WTDcujFHjTWjlJYWIzkJe8y9XmKpj9XozE0,22918
 arrayview/_session.py,sha256=-Jems6lGOVU3uLs4Uq1ggIfY-qTrAXNzpUk6nMbuTBA,35616
 arrayview/_session_spec.py,sha256=mKDfMRsPYQdEmN9hLXmDU_9N7etiDyBXr8mz-fB8QBo,6825
 arrayview/_shell.html,sha256=vNa2Kiwx_eoB5H329jolYafLhwJDCH9DsJafBqvVMWU,13194
-arrayview/_source_safety.py,sha256=EetyfZFZrVYWV3bdFe4sZovrcdc8Fkr9vqLxc6oUBxI,27635
+arrayview/_source_safety.py,sha256=cI7JAL7DWYuxuB_LnYExvJZaICX2R2qJEJWD1M0z_gg,27664
 arrayview/_synthetic_mri.py,sha256=CNL-2WC835i6WCqkvmWBCO6WQ5w7HE5trNb8OyEfe64,7365
 arrayview/_torch.py,sha256=13sqIMCUu_-b9SQ9KfDCExDz2UMStL87EDVjnbJxAEo,7536
 arrayview/_tutorial.py,sha256=2zZHJGJDa4n30GE1-9ADjKFAifGBH9vvHXP4uDt7BaA,19547
@@ -46,14 +46,14 @@ arrayview/_vectorfield.py,sha256=eDqMCMEGjO8Jdt-6Auh01cz3WD9dbF7xYUWD9xHAf1E,811
 arrayview/_viewer.html,sha256=aiHPSbCCtj90EnHV0nJ7kh8YkxAaUmzdDYJGW5KC0Zg,2372368
 arrayview/_vscode.py,sha256=EKnGN2zrjlybc4FQOmYA8BvYdtkcJbLHDEdgtvO7ul4,837
 arrayview/_vscode_browser.py,sha256=VCH9JpAAjFuhO0wQe8tIGjAL5837AXg_bpmBFtWOQqc,20573
-arrayview/_vscode_extension.py,sha256=aXkuw5lyqahOjK5OJfKYySFPX5yt1jSEUgqvoHiF3ZE,53156
+arrayview/_vscode_extension.py,sha256=tF62xp_zVDMexlPtAZ7wKvKCKakdygmf3IGIcICoKeE,53156
 arrayview/_vscode_signal.py,sha256=N3PCHG6-3tCEc_tHLjg2dhSEQ2EnF_psE2IJRBpAuac,54938
 arrayview/_watch.py,sha256=PxxS_5hcj_S6xQf9Ep4p1HLRkrI5iDMh1aRa4olV7ew,1873
-arrayview/arrayview-opener.vsix,sha256=dga4sUvFEK8N-UjKcmhYW0SDedci83Q2gx4-XB8BoTY,61308
+arrayview/arrayview-opener.vsix,sha256=BpRLXxm4j9gc34xusHzE80g01m6CvIK_fzf3ApgS5xE,61442
 arrayview/gsap.min.js,sha256=VGihm4idI0E1uqrWezWsiScB9F_jMosn7qs6pPSkeac,72304
 arrayview/todo.md,sha256=KhnRzpn6_jezR0nDDB61-zhox-rbOmEGW-A7Z0_7FnU,622
-arrayview-0.47.3.dist-info/METADATA,sha256=lxECYFGKs3cRc80zXrP19y9TYQPbBHW-bi4qFf5hWas,2288
-arrayview-0.47.3.dist-info/WHEEL,sha256=W3fkpkm7-wf9vBI5Z-7s0eWkeM-spu78I8Neb98DeEg,87
-arrayview-0.47.3.dist-info/entry_points.txt,sha256=-0s08axutXkTbINiKs0Q7iv-33aWuTaamUg2q2-NyQ4,60
-arrayview-0.47.3.dist-info/licenses/LICENSE,sha256=34OivjM9faB2QaPjZpMRTIiSx31V3U9cEyQ6F2k-bH0,1062
-arrayview-0.47.3.dist-info/RECORD,,
+arrayview-0.47.4.dist-info/METADATA,sha256=V3wlriyNB8GhY_UZwcin_BktoAU6pkum8vDVg6FYVCY,2288
+arrayview-0.47.4.dist-info/WHEEL,sha256=W3fkpkm7-wf9vBI5Z-7s0eWkeM-spu78I8Neb98DeEg,87
+arrayview-0.47.4.dist-info/entry_points.txt,sha256=-0s08axutXkTbINiKs0Q7iv-33aWuTaamUg2q2-NyQ4,60
+arrayview-0.47.4.dist-info/licenses/LICENSE,sha256=34OivjM9faB2QaPjZpMRTIiSx31V3U9cEyQ6F2k-bH0,1062
+arrayview-0.47.4.dist-info/RECORD,,