arrayview 0.31.3__tar.gz → 0.32.0__tar.gz

{arrayview-0.31.3 → arrayview-0.32.0}/.mex/context/lifecycle.md

@@ -16,7 +16,7 @@ edges:
     condition: when component boundaries or display routing need broader context
   - target: context/stack.md
     condition: when VS Code, FastAPI, WebSocket, or packaging details are needed
-last_updated: 2026-06-19
+last_updated: 2026-07-14
 ---
 
 # Lifecycle
@@ -60,8 +60,10 @@ This contract describes who owns the backend, when it starts, and what closes it
 
 - Remote or tunnel launches may persist when `--serve` or tunnel display ownership requires it.
 - VS Code tunnel display uses forwarded localhost URLs; the extension should configure the port, promote privacy when available, and resolve the URL with `asExternalUri`.
-- With multiple registered tunnel windows, a missing or stale `ARRAYVIEW_WINDOW_ID` uses the shared broadcast signal; only the focused VS Code window may claim it.
+- With multiple registered tunnel windows, a missing `ARRAYVIEW_WINDOW_ID` first recovers the exact live registration from the terminal's IPC hook. Only when no exact registration exists does it use the shared focused-window broadcast fallback.
 - An exact registered `ARRAYVIEW_WINDOW_ID` wins; do not redirect it to a newer same-parent registration because live tunnel windows can share ancestry.
+- Protocol request claims are atomic across extension hosts. Compatibility queue copies with the same request ID must never open in a sibling window or overwrite a terminal ACK.
+- Tunnel `asExternalUri` results must be non-loopback. Remote-SSH may legitimately resolve to a local forwarded URL and must not be subjected to tunnel-only public-port commands.
 - Plain SSH should use `localhost` forwarding guidance and stay transient unless a shared server was explicitly requested.
 
 ## Shared Rules
@@ -76,6 +78,7 @@ This contract describes who owns the backend, when it starts, and what closes it
   tab cannot invalidate another tab that shares the same SID.
 - A VS Code readiness ACK includes the live opener version and is terminal only
   after the requested SID exists and the viewer reports its first rendered frame.
+- Existing-server tunnel loads publish a pending SID before loading large files, so port resolution can overlap disk I/O. Pending metadata probes return immediately and the WebSocket waits on the shared pending-session event.
 - Older ArrayView packages must not delete or downgrade a newer installed opener.
 - Tunnel registration cleanup must not remove live same-tunnel sibling windows.
 - Explicit cleanup wins over implicit disappearance.

{arrayview-0.31.3 → arrayview-0.32.0}/.mex/context/project-state.md

@@ -7,7 +7,7 @@ triggers:
   - "recent work"
   - "active feature"
   - "shipped recently"
-last_updated: 2026-07-13
+last_updated: 2026-07-20
 ---
 
 # Project State
@@ -20,8 +20,8 @@ last_updated: 2026-07-13
 - Rendering pipeline: colormaps, complex modes, mosaic, RGB/RGBA, projections, overlays
 - Backend transport: FastAPI HTTP/WebSocket is the single viewer transport; shared helpers keep route modules small for metadata/analysis, compare/diff, overlay compositing, and vector field layout/arrow sampling.
 - NIfTI spatial metadata, RAS resampling
-- Directory collections are header-scanned and lazy by default: compatible files form a dense virtual stack, mixed shapes use a ragged collection, and `--load lazy|eager` plus `--stack-policy auto|dense|ragged` make both choices explicit. Compressed NIfTI volumes use a byte-bounded LRU cache; `view_dir()` exposes the same controls.
-- VS Code extension v0.14.41 — stable per-window routing, queued concurrent requests, remote-only tunnel claims, live opener-version ACKs, first-frame readiness, and immediate local-backend session release. An installed-but-stale extension host now fails with a clear one-time reload instruction instead of opening an unverified blank tab; older cached ArrayView packages never delete a newer opener.
+- Directory collections are header-scanned and lazy by default: compatible files form a dense virtual stack, mixed shapes use a ragged collection, and `--load lazy|eager` plus `--stack-policy auto|dense|ragged` make both choices explicit. Supported 3D `.nii.gz` stacks now return the requested axial plane while the same one-pass decode finishes in the byte-bounded LRU cache; unsupported layouts fall back safely. Patient changes show a centered loading card until the matching frame arrives. `view_dir()` exposes the same collection controls.
+- VS Code extension v0.14.43 — exact tunnel-window recovery from the terminal IPC hook, atomic cross-window request claims, non-loopback tunnel URL enforcement, queued concurrent requests, remote-only tunnel claims, live opener-version ACKs, first-frame readiness, and immediate local-backend session release. Successful port-public promotion is cached per external tunnel URL, and existing-server tunnel loads overlap port setup with pending background data loading.
 - Colorbar refactor: `ColorBar` JS class partially migrated (in progress)
 - Colormap picker: `c` opens an expanded colorbar-island grid without changing the colormap; subsequent `c` taps cycle, hover/hjkl/arrows live-preview, Enter/click commits, Esc cancels, and auto-dismiss pauses while hovered
 - Cold-start loading spinner in VS Code and native shell
@@ -60,6 +60,10 @@ last_updated: 2026-07-13
 
 ## Recently Completed
 
+- Jupyter inline viewports automatically fit ortho content and restore the
+  normal `height` on exit. `mode_heights` remains available for explicit
+  overrides. Direct, proxied, multi-array, and IJulia inline paths share the
+  same mode-change bridge.
 - ROI keybind changed from `r` to `Shift+R` (`R`); rotate/flip is now `r`, transpose is `t`
 - Crossfade animation added to rotate/transpose transitions
 - `--version` flag and version string in help overlay
@@ -86,6 +90,7 @@ last_updated: 2026-07-13
 
 ## In Progress
 
+- VS Code tunnel opener v0.14.43 is installed on disk and fully covered by focused lifecycle/ACK tests; active 0.14.42 extension hosts still need one window reload before post-change live timing and multi-window verification.
 - Smooth immersive transition — stale scrub geometry handoff is fixed, immersive overlay fade-in is held until after the class switch, shared slim colorbar returns through `drawSlimColorbar()` on reverse, and active scrub suppresses minimap/overflow/drag side effects. Single-pane scrub now targets the actual centered immersive viewport rect instead of a hardcoded corner box, the dimbar stays above the pane during scrub, the shared colorbar sits behind the growing pane, and the phantom extra `av-view-wrap` footprint in normal mode was removed by rebinding `NormalLayout` to the real `#viewer` canvas. Cross-mode parity and deeper reverse-pinch validation still need manual verification.
 - ROI + qMRI integration refinements: floodfill not yet supported on qMRI panes; per-pane stats are re-fetched on each ROI draw but not updated on slice scroll
 

{arrayview-0.31.3 → arrayview-0.32.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: arrayview
-Version: 0.31.3
+Version: 0.32.0
 Summary: Fast multi-dimensional array viewer
 Project-URL: Home, https://github.com/oscarvanderheide/arrayview
 Project-URL: Source, https://github.com/oscarvanderheide/arrayview
@@ -51,7 +51,10 @@ Curious? Give it a try with
 uvx arrayview your_array.npy
 ```
 
+Press `v` for the three-plane ortho view. `Shift+3` replaces the current slice,
+or all three ortho panes, with interactive 3D cutaway renders.
+
 
 Check the [docs](https://oscarvanderheide.github.io/arrayview/) to learn more. 
 
-**Warning**: Arrayview is still under active development. Things may break or change without warning.
+**Warning**: Arrayview is still under active development. Things may break or change without warning.

{arrayview-0.31.3 → arrayview-0.32.0}/README.md

@@ -15,7 +15,10 @@ Curious? Give it a try with
 uvx arrayview your_array.npy
 ```
 
+Press `v` for the three-plane ortho view. `Shift+3` replaces the current slice,
+or all three ortho panes, with interactive 3D cutaway renders.
+
 
 Check the [docs](https://oscarvanderheide.github.io/arrayview/) to learn more. 
 
-**Warning**: Arrayview is still under active development. Things may break or change without warning.
+**Warning**: Arrayview is still under active development. Things may break or change without warning.

{arrayview-0.31.3 → arrayview-0.32.0}/docs/loading.md

@@ -54,6 +54,8 @@ Key parameters:
 | `name` | str | Label shown in the viewer tab |
 | `port` | int | Server port (default 8123 for Python API, 8000 for CLI) |
 | `window` | str \| None | How to open the viewer (see below) |
+| `height` | int | Default inline notebook height in pixels |
+| `mode_heights` | dict | Inline height overrides, e.g. `{"ortho": 360, "qmri": 480}` |
 | `rgb` | bool | Treat last/first axis as RGB/RGBA channels |
 | `overlay` | array or list | Arrays composited as overlays |
 
@@ -67,6 +69,9 @@ Key parameters:
 | `"vscode"` | VS Code tab |
 | `"inline"` | Inline IFrame (Jupyter / VS Code notebook) |
 
+Inline ortho view automatically removes unused height. `mode_heights` is only
+needed to override the automatic size.
+
 ## File Picker
 
 `Cmd/Ctrl+O` or `P` opens the file picker.
@@ -117,10 +122,11 @@ up front.
 Pattern collections, named overlays, multiple overlays, and `--overlay-dir`:
 [Stack and Overlay Collections](stack-overlays.md).
 
-## NIfTI Series (4D/5D from a directory)
+## NIfTI Series
 
-Stack a directory of NIfTI files into a single lazy 4D/5D array — only the
-viewed slice is loaded, so RAM stays bounded regardless of series size.
+Stack a directory of NIfTI files into a single lazy 4D/5D array. Patient files
+are loaded only when needed, and the memory cache stays bounded regardless of
+series size.
 
 ```bash
 uvx arrayview patients/
@@ -132,27 +138,32 @@ Discovers `.nii`/`.nii.gz` recursively, groups by immediate parent folder
 One file per patient → 4D `(*vol, P)`. The viewer opens with X/Y on screen,
 Z as primary scroll, patient index as a slider.
 
-Multiple files per patient (e.g. `t1`, `t2`, `flair`) → use `--select`:
+For multiple files per patient, use explicit `--stack` patterns:
 
 ```bash
-uvx arrayview patients/ --select '*t1*' --select '*t2*' --select '*flair*'
+uvx arrayview --stack \
+  "patients/*/*t1*.nii.gz" \
+  "patients/*/*t2*.nii.gz" \
+  "patients/*/*flair*.nii.gz"
 ```
 
-Each `--select` pattern picks one file per patient (fnmatch on basename).
-Produces 5D `(*vol, P, M)` with modality as the last axis. Every patient
-must match exactly one file per pattern.
+More examples: [Stack and Overlay Collections](stack-overlays.md).
 
-Python API:
+Patient folders with no NIfTI files (e.g. only `.dcm`) raise an error —
+convert DICOM to NIfTI first (e.g. `dcm2niix`).
 
-```python
-from arrayview import view_dir
+### First image from compressed patients
 
-view_dir("patients/")
-view_dir("patients/", select=["*t1*", "*t2*", "*flair*"])
-```
+For a normal 3D `.nii.gz` patient, ArrayView shows the requested axial slice as
+soon as that slice has been unpacked. It keeps unpacking the rest of the same
+file in the background and saves the completed volume in the existing memory
+cache. The file is not unpacked a second time.
 
-Patient folders with no NIfTI files (e.g. only `.dcm`) raise an error —
-convert DICOM to NIfTI first (e.g. `dcm2niix`).
+This shortens the visible wait, but it does not make gzip random-access. A slice
+near the middle still requires reading roughly the first half of the file.
+Side views, 4D files, and unusual orientations fall back to loading the complete
+volume first so their data remains correct. Moving quickly between patients
+stops outdated background work instead of building a long loading queue.
 
 ## Zarr
 

{arrayview-0.31.3 → arrayview-0.32.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "arrayview"
-version = "0.31.3"
+version = "0.32.0"
 description = "Fast multi-dimensional array viewer"
 readme = { file = "README.md", content-type = "text/markdown" }
 requires-python = ">=3.12"

{arrayview-0.31.3 → arrayview-0.32.0}/src/arrayview/__init__.py

@@ -7,14 +7,12 @@ __all__ = [
     "arrayview",
     "view",
     "view_batch",
-    "view_dir",
-    "view_dir_patterns",
     "zarr_chunk_preset",
 ]
 
 
 def __getattr__(name: str):
-    if name in {"arrayview", "view", "view_dir", "view_dir_patterns", "ViewHandle"}:
+    if name in {"arrayview", "view", "ViewHandle"}:
         from arrayview import _launcher
 
         return getattr(_launcher, name)