arrayview 0.50.1__tar.gz → 0.51.1__tar.gz

{arrayview-0.50.1 → arrayview-0.51.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: arrayview
-Version: 0.50.1
+Version: 0.51.1
 Summary: Fast multi-dimensional array viewer
 Project-URL: Home, https://github.com/oscarvanderheide/arrayview
 Project-URL: Source, https://github.com/oscarvanderheide/arrayview
@@ -39,6 +39,8 @@ Description-Content-Type: text/markdown
 
 _This is my array viewer. There are many like it, but this one is mine._ 
 
+<img src="docs/teaser.gif" alt="ArrayView: scrolling a volume, switching colormaps, three planes, and a difference view" width="800">
+
 Arrayview lets you scroll through multi-dimensional arrays.
 
 Open it from the shell, from Python, Julia, or Matlab, or inside a Jupyter notebook. Use it locally or over SSH. 

{arrayview-0.50.1 → arrayview-0.51.1}/README.md

@@ -2,6 +2,8 @@
 
 _This is my array viewer. There are many like it, but this one is mine._ 
 
+<img src="docs/teaser.gif" alt="ArrayView: scrolling a volume, switching colormaps, three planes, and a difference view" width="800">
+
 Arrayview lets you scroll through multi-dimensional arrays.
 
 Open it from the shell, from Python, Julia, or Matlab, or inside a Jupyter notebook. Use it locally or over SSH. 

{arrayview-0.50.1 → arrayview-0.51.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "arrayview"
-version = "0.50.1"
+version = "0.51.1"
 description = "Fast multi-dimensional array viewer"
 readme = { file = "README.md", content-type = "text/markdown" }
 requires-python = ">=3.12"

{arrayview-0.50.1 → arrayview-0.51.1}/src/arrayview/_io.py

@@ -1452,7 +1452,7 @@ def _collection_pattern_paths(pattern):
     return paths
 
 
-def _explicit_case_files(patterns):
+def _explicit_case_files(patterns, keep_order=False):
     """Plain file paths given as several patterns, or None.
 
     An unquoted ``--match dir/*/maps.nii`` reaches us already expanded by the
@@ -1467,7 +1467,7 @@ def _explicit_case_files(patterns):
     paths = [os.path.abspath(p) for p in patterns if _is_supported_collection_path(p)]
     if len(paths) != len(patterns) or len(set(paths)) != len(paths):
         return None
-    return sorted(paths)
+    return paths if keep_order else sorted(paths)
 
 
 def _distinguishing_path_parts(paths):
@@ -1720,6 +1720,7 @@ def load_dir_collection(
     stack="auto",
     scan_progress=None,
     exclude_cases=None,
+    keep_order=False,
 ):
     """Load recursive collection patterns as aligned lazy image/overlay stacks.
 
@@ -1730,7 +1731,8 @@ def load_dir_collection(
     *case_regex*, files are paired by the regex's named ``case`` group instead.
     *exclude_cases* removes known case ids before any image or overlay data is
     opened. It is used by the interactive CLI after the user accepts a partial
-    overlay match.
+    overlay match. *keep_order* stacks an explicit file list in the order
+    given instead of sorted.
     """
     if not base_patterns:
         raise ValueError("--match requires at least one positional image pattern.")
@@ -1753,7 +1755,7 @@ def load_dir_collection(
             raise ValueError("; ".join(missing))
         base_matrix = [[by_case[case] for by_case in base_maps] for case in case_ids]
     else:
-        explicit_cases = _explicit_case_files(base_patterns)
+        explicit_cases = _explicit_case_files(base_patterns, keep_order=keep_order)
         base_lists = (
             [explicit_cases]
             if explicit_cases is not None

{arrayview-0.50.1 → arrayview-0.51.1}/src/arrayview/_launcher.py

@@ -1323,6 +1323,7 @@ def _load_session_from_filepath(
     dir_exclude_cases: list[str] | None = None,
     collection_load: str = "lazy",
     collection_stack: str = "auto",
+    collection_keep_order: bool = False,
     background: bool = False,
     expected_server_id: str | None = None,
     native_request_id: str | None = None,
@@ -1365,6 +1366,7 @@ def _load_session_from_filepath(
         payload["dir_exclude_cases"] = dir_exclude_cases or []
         payload["load"] = collection_load
         payload["stack"] = collection_stack
+        payload["keep_order"] = collection_keep_order
     if notify and compare_sids:
         payload["compare_sid"] = compare_sids[0]
         payload["compare_sids"] = _join_query_values(compare_sids)
@@ -1686,6 +1688,7 @@ def _register_cli_session_with_existing_server_impl(
     dir_exclude_cases: list[str] | None = None,
     collection_load: str = "lazy",
     collection_stack: str = "auto",
+    collection_keep_order: bool = False,
     overlay_names: list[str] | None = None,
     background_base: bool = False,
     expected_server_id: str | None = None,
@@ -1741,6 +1744,7 @@ def _register_cli_session_with_existing_server_impl(
         dir_exclude_cases=dir_exclude_cases,
         collection_load=collection_load,
         collection_stack=collection_stack,
+        collection_keep_order=collection_keep_order,
         background=background_base,
         expected_server_id=expected_server_id,
         native_request_id=native_request_id,
@@ -1838,6 +1842,7 @@ def _handle_cli_existing_server(
     dir_exclude_cases: list[str] | None = None,
     collection_load: str = "lazy",
     collection_stack: str = "auto",
+    collection_keep_order: bool = False,
     overlay_names: list[str] | None = None,
     cleanup_dir: str | None = None,
     source_staging_dirs: dict[str, str] | None = None,
@@ -1866,6 +1871,7 @@ def _handle_cli_existing_server(
             dir_exclude_cases=dir_exclude_cases,
             collection_load=collection_load,
             collection_stack=collection_stack,
+            collection_keep_order=collection_keep_order,
             overlay_names=overlay_names,
             background_base=(
                 is_remote
@@ -1954,6 +1960,7 @@ def _handle_cli_existing_server(
                     dir_exclude_cases=dir_exclude_cases,
                     collection_load=collection_load,
                     collection_stack=collection_stack,
+                    collection_keep_order=collection_keep_order,
                     overlay_names=overlay_names,
                     source_staging_dirs=source_staging_dirs,
                 )
@@ -2084,6 +2091,7 @@ def _handle_cli_spawned_daemon(
     dir_exclude_cases: list[str] | None = None,
     collection_load: str = "lazy",
     collection_stack: str = "auto",
+    collection_keep_order: bool = False,
     overlay_names: list[str] | None = None,
     cleanup_dir: str | None = None,
     source_staging_dirs: dict[str, str] | None = None,
@@ -2147,6 +2155,7 @@ def _handle_cli_spawned_daemon(
                 dir_exclude_cases=dir_exclude_cases,
                 collection_load=collection_load,
                 collection_stack=collection_stack,
+                collection_keep_order=collection_keep_order,
                 overlay_names=resolved_overlay_names,
                 cleanup_dir=cleanup_dir,
                 source_staging_dirs=source_staging_dirs,
@@ -2202,6 +2211,7 @@ def _handle_cli_spawned_daemon(
             f" dir_exclude_cases={repr(dir_exclude_cases)},"
             f" collection_load={repr(collection_load)},"
             f" collection_stack={repr(collection_stack)},"
+            f" collection_keep_order={repr(collection_keep_order)},"
             f" cleanup_dir={repr(cleanup_dir)},"
             f" source_staging_dirs={repr(source_staging_dirs or {})},"
             f" watch={watch},"
@@ -4729,6 +4739,7 @@ def _serve_daemon(
     dir_exclude_cases: list[str] | None = None,
     collection_load: str = "lazy",
     collection_stack: str = "auto",
+    collection_keep_order: bool = False,
     cleanup_dir: str | None = None,
     source_staging_dirs: dict[str, str] | None = None,
     watch: bool = False,
@@ -4868,6 +4879,7 @@ def _serve_daemon(
                     exclude_cases=dir_exclude_cases,
                     load=collection_load,
                     stack=collection_stack,
+                    keep_order=collection_keep_order,
                 )
                 collection_spatial_ndim = len(_summary["spatial_shape"])
             elif (filepath.endswith(".npz") or filepath.endswith(".mat")) and not cleanup:
@@ -6052,6 +6064,27 @@ def arrayview():
             "stacking: a directory of arrays is stacked either way. It selects "
             "which files form the collection."
         )
+    if (
+        args.files
+        and len(args.files) > 4
+        and not args.stack_mode
+        and not (
+            args.compare
+            or args.overlay
+            or args.vectorfield
+            or args.watch
+            or args.rgb
+            or args.relay
+        )
+    ):
+        # Too many for a side-by-side compare: stack them along a new last
+        # axis, one case per file, as --match does for explicit file lists.
+        args.stack_mode = True
+        args.keep_file_order = True
+        print(
+            f"[ArrayView] {len(args.files)} files: opened as one stack; "
+            "step through the last dimension to switch files."
+        )
     if args.dry_run and not args.stack_mode:
         parser.error("--dry-run requires --match.")
     excluded_cases = set()
@@ -6098,9 +6131,10 @@ def arrayview():
             dims_override = (0, 1)
     if not args.serve and not args.kill and not args.files:
         _configure_tutorial_args(args)
-    if args.files and len(args.files) > 6 and not args.stack_mode:
+    if args.files and len(args.files) > 4 and not args.stack_mode:
         parser.error(
-            "At most six FILE arguments are supported; concat arrays first for larger compare sets."
+            "More than four FILE arguments open as one stack, which does not "
+            "support --compare, --overlay, --vectorfield, --watch, --rgb, or --relay."
         )
     if args.compare and len(args.files) > 1 and not args.stack_mode:
         parser.error("Use either positional compare files or --compare, not both.")
@@ -6310,6 +6344,7 @@ def arrayview():
                         stack=args.stack_policy or "auto",
                         scan_progress=scan_progress.update,
                         exclude_cases=excluded_cases,
+                        keep_order=getattr(args, "keep_file_order", False),
                     )
                 finally:
                     scan_progress.finish()
@@ -6683,6 +6718,7 @@ def arrayview():
                 dir_exclude_cases=sorted(excluded_cases),
                 collection_load=args.load,
                 collection_stack=args.stack_policy or "auto",
+                collection_keep_order=getattr(args, "keep_file_order", False),
                 cleanup_dir=getattr(args, "_tutorial_cleanup_dir", None),
                 source_staging_dirs=(
                     source_staging_dirs if not args.stack_mode else None
@@ -6723,6 +6759,7 @@ def arrayview():
             dir_exclude_cases=sorted(excluded_cases),
             collection_load=args.load,
             collection_stack=args.stack_policy or "auto",
+            collection_keep_order=getattr(args, "keep_file_order", False),
             source_staging_dirs=(
                 source_staging_dirs if not args.stack_mode else None
             ),

{arrayview-0.50.1 → arrayview-0.51.1}/src/arrayview/_routes_loading.py

@@ -227,6 +227,7 @@ def register_loading_routes(app, *, notify_shells, setup_rgb) -> None:
                 tuple(str(case) for case in body.get("dir_exclude_cases", [])),
                 body.get("load", "lazy"),
                 body.get("stack", "auto"),
+                bool(body.get("keep_order", False)),
             )
             for existing in [] if requested_sid else SESSIONS.values():
                 if getattr(existing, "collection_identity", None) == collection_identity:
@@ -440,6 +441,7 @@ def register_loading_routes(app, *, notify_shells, setup_rgb) -> None:
                         exclude_cases=body.get("dir_exclude_cases", []),
                         load=body.get("load", "lazy"),
                         stack=body.get("stack", "auto"),
+                        keep_order=bool(body.get("keep_order", False)),
                     )
                 elif filepath.endswith(".npz") or filepath.endswith(".mat"):
                     _array_keys = await asyncio.to_thread(list_array_keys, filepath)

{arrayview-0.50.1 → arrayview-0.51.1}/src/arrayview/_routes_query.py

@@ -429,7 +429,7 @@ def register_query_routes(app, *, get_session_or_404, pil_image, pil_imageops) -
             info["overlay_labels"] = []
             try:
                 if np.issubdtype(session.data.dtype, np.integer):
-                    labels = np.unique(session.data)
+                    labels = np.unique(_overlay_label_sample(session))
                     labels = labels[labels > 0]
                     if labels.size <= 16:
                         info["overlay_labels"] = [int(value) for value in labels]
@@ -531,6 +531,18 @@ def register_query_routes(app, *, get_session_or_404, pil_image, pil_imageops) -
         )
 
 
+def _overlay_label_sample(session):
+    """Overlay values to read label ids from: the whole array, or only the
+    first case of a collection (reading every case would stall opening; the
+    viewer adds labels found in other cases as they are visited)."""
+    spatial = getattr(session, "collection_spatial_ndim", None)
+    shape = tuple(session.shape)
+    if spatial is None or not (0 < spatial < len(shape)):
+        return np.asarray(session.data)
+    index = (slice(None),) * spatial + (0,) * (len(shape) - spatial)
+    return np.asarray(session.data[index])
+
+
 def _overlay_slice_counts(ov_session, base_shape, dim_x, dim_y, axis, idx_list):
     """Count overlay pixels per label on every slice along ``axis``."""
     n = int(base_shape[axis])
@@ -555,6 +567,8 @@ def _overlay_slice_counts(ov_session, base_shape, dim_x, dim_y, axis, idx_list):
         return empty
     kept = [a for a in base_axes if a in (dim_x, dim_y, axis)]
     if axis in kept:
+        # Ragged collections return this case's own size, not the max-shape facade.
+        n = int(vol.shape[kept.index(axis)])
         vol = np.moveaxis(vol, kept.index(axis), 0).reshape(n, -1)
     else:
         # The overlay has no such axis: it looks the same on every slice.