arrayview 0.29.2__tar.gz → 0.31.0__tar.gz

arrayview-0.31.0/.github/workflows/launch-contracts.yml

@@ -0,0 +1,62 @@
+name: Launch contracts
+
+on:
+  pull_request:
+    paths:
+      - src/arrayview/**
+      - tests/**
+      - vscode-extension/**
+      - pyproject.toml
+      - uv.lock
+      - .github/workflows/launch-contracts.yml
+  push:
+    branches: [main]
+    paths:
+      - src/arrayview/**
+      - tests/**
+      - vscode-extension/**
+      - pyproject.toml
+      - uv.lock
+      - .github/workflows/launch-contracts.yml
+
+permissions:
+  contents: read
+
+jobs:
+  planner-and-lifecycle:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - uses: astral-sh/setup-uv@v6
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "22"
+      - run: uv sync --frozen --group dev --group test
+      - name: Python launch contracts
+        run: >-
+          uv run pytest
+          tests/test_launch_plan.py
+          tests/test_launch_diagnostics.py
+          tests/test_invocation_contract_matrix.py
+          tests/test_instance_registry.py
+          tests/test_server_identity_status.py
+          tests/test_safe_server_stop.py
+          tests/test_view_handle_lifecycle.py
+          tests/test_view_launch_execution.py
+          tests/test_vscode_ack_protocol.py
+          tests/test_display_opener_results.py
+          tests/test_doctor_commands.py
+          tests/test_cli.py
+          tests/test_lifecycle_contract.py
+          -q
+      - name: VS Code extension contracts
+        run: node vscode-extension/test_lifecycle_helpers.js
+      - name: VS Code extension syntax
+        run: node --check vscode-extension/extension.js

{arrayview-0.29.2 → arrayview-0.31.0}/.mex/context/project-state.md

@@ -20,7 +20,7 @@ last_updated: 2026-06-30
 - 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
-- NIfTI series: `--stack-nifti DIR` + `--select PATTERN` stacks a directory of same-shape NIfTI files into a lazy 4D/5D array; `view_dir()` Python helper; recursive patient-folder grouping, LRU volume cache, spatial meta from first file
+- 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 v0.14.27 — stable window ID via `EnvironmentVariableCollection`; `arrayview.openInFloatingWindow` setting moves new tabs to a floating window; `view(arr, floating=True)` and `arrayview file.npy --floating` open in a floating window per-call regardless of global setting; remote/tunnel display uses the same forwarded HTTP/WebSocket path as local VS Code; floating mode uses a single persistent shell hub panel (`_shell.html`) so all arrays share one floating window as tabs instead of opening separate windows; second CLI calls inject tabs via `new_tab` postMessage relay (extension -> hub wrapper -> shell iframe)
 - 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
@@ -32,8 +32,25 @@ last_updated: 2026-06-30
 - qMRI map toggle (`_islandToggleQmriMap`) fade animation now covers dimbar and array-name in addition to panes and colorbars
 - Segmentation menu shares the ROI layout (yellow accent, magnifier action icon, common `#export-overlay` modal). Pre-activation shows a pulsing "nnInteractive · connecting" row that morphs into the normal shape toolbar once `/seg/activate` resolves
 - Overlays are a plugin tile (`OV`): per-overlay row with colour swatch, editable label, eye toggle, × delete; shared opacity slider; `+ add overlay` opens a filesystem picker rooted at the launched file's directory
+- The floating overlay HUD is reconciled as soon as startup loading ends, so it
+  is visible on first load and `/ o` toggles it correctly from the first press.
+  Its drag grip allows viewport-clamped repositioning that survives mode and
+  layout reconciliation for the current viewer session. Hovering a visible row
+  focuses that mask and dims the other visible overlays across normal, compare,
+  multiview, and qMRI render paths. The HUD and overlay drawer can switch masks
+  between filled regions and outline-only contours.
 - Vector field is a plugin tile (`VF`): row with visibility toggle + density/length sliders bi-directionally wired to the `[ ] { }` keyboard commands
-- CLI `--overlay FILE` can be repeated to load multiple overlays at launch
+- CLI `--overlay FILE` can be repeated to load multiple overlays at launch;
+  unnamed overlays use the filename stem and `NAME=FILE` supplies an explicit
+  HUD label.
+- Stack collections support `--overlay-dir PATTERN` to discover per-case mask
+  filenames as sparse overlay roles; missing masks render as empty and common
+  patient/modality directory layouts pair automatically. `--case-regex` remains
+  an override for unusual layouts. CLI header scans show an in-place file counter
+  and elapsed time on interactive terminals.
+- Reused collection sessions are protected by per-tab leases, including their
+  overlay sessions, and VS Code opener readiness now verifies the requested
+  session metadata before acknowledging `backend_ready`.
 - Filesystem picker endpoint (`GET /fs/list`) clamped to `$HOME`. Accepts `base_sid` + `mode` (`overlay` | `vectorfield`) to filter entries by a cheap header-shape peek (`.npy`, `.nii`/`.nii.gz`, `.h5`, `.zarr`); overlay mode requires identical shape, vectorfield mode requires base shape plus one axis of size 3
 - Island collapse affordance: inline `~` at the island's top-right animates the panel into the bottom-left `~` hint circle; external `~` hint only visible while the island is actually collapsed. New `/` hint circle at bottom-right opens the tool menu
 - Compare center tool menu: `/` now re-opens the last-used compare center mode from the tool menu, while compare pane header buttons select diff / overlay / wipe directly. Eligible two-array compare layouts can switch into a big-left arrangement with a wider center pane, and the diff colorbar now matches that center-pane width.

{arrayview-0.29.2 → arrayview-0.31.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: arrayview
-Version: 0.29.2
+Version: 0.31.0
 Summary: Fast multi-dimensional array viewer
 Project-URL: Home, https://github.com/oscarvanderheide/arrayview
 Project-URL: Source, https://github.com/oscarvanderheide/arrayview

{arrayview-0.29.2 → arrayview-0.31.0}/docs/comparing.md

@@ -37,7 +37,14 @@ Or use the file picker (`Cmd/Ctrl+O`) or drag-and-drop.
 uvx arrayview volume.nii.gz --overlay mask.nii.gz
 ```
 
-Binary mask (0/1), same spatial shape. `[`/`]` adjusts blend opacity. Multiple overlays get automatic palette colors.
+Binary mask (0/1), same spatial shape. `[`/`]` adjusts blend opacity. Multiple overlays get automatic palette colors. Hover an overlay HUD row to focus that mask while dimming the others. Use the overlay HUD or `/ o` to switch between filled masks and outline-only contours.
+
+For cohort review, use `--stack` so image and overlay patterns are paired into
+aligned stacks:
+
+```bash
+uvx arrayview --stack "data/**/*_0000.nii.gz" --overlay "gt=data/**/labels/*.nii.gz"
+```
 
 ## Vector field
 

{arrayview-0.29.2 → arrayview-0.31.0}/docs/configuration.md

@@ -46,3 +46,6 @@ Explicit `--window` flag > `ARRAYVIEW_WINDOW` env var > config file > built-in d
 | `jupyter` | Jupyter / IPython notebook kernel |
 | `ssh` | SSH session without VS Code |
 | `julia` | Julia via PythonCall / PyCall |
+
+MATLAB uses the detected terminal, VS Code, SSH, or remote route. Local MATLAB
+prefers a native window when available. See [MATLAB and Julia](foreign-hosts.md).

arrayview-0.31.0/docs/foreign-hosts.md

@@ -0,0 +1,104 @@
+# MATLAB and Julia
+
+ArrayView uses the Python environment selected by the host application.
+
+## MATLAB
+
+Select a Python environment with ArrayView installed, then import and call it:
+
+```matlab
+pyenv(Version="/path/to/python")
+py.importlib.import_module("arrayview");
+
+h = py.arrayview.view(A);
+```
+
+Local MATLAB follows the normal display selection and prefers a native window
+when available. MATLAB started through SSH or VS Code follows that environment's
+browser or VS Code route.
+
+The array is converted to NumPy before registration. Keep `h` when explicit
+cleanup is needed:
+
+```matlab
+h.close()
+```
+
+## Julia
+
+PythonCall:
+
+```julia
+using PythonCall
+
+arrayview = pyimport("arrayview")
+h = arrayview.view(A)
+```
+
+PyCall:
+
+```julia
+using PyCall
+
+arrayview = pyimport("arrayview")
+h = arrayview.view(A)
+```
+
+Julia currently supports one array per `view()` call. Call `view()` again for
+another array.
+
+ArrayView copies the array to a temporary NumPy file and starts or reuses a
+separate Python server process. This avoids blocking on Julia's Python lock and
+lets the viewer survive after the call returns. The returned value is a Python
+`ViewHandle` wrapper with `url`, `sid`, `port`, `update()`, and `close()`.
+
+```julia
+h.close()
+```
+
+## IJulia
+
+Use the same PythonCall or PyCall code in an IJulia notebook. ArrayView displays
+an inline iframe by default. Inline display is a side effect; the call may return
+`nothing` instead of a handle.
+
+## Display routing
+
+| Host | Default display |
+|------|-----------------|
+| Local desktop | Native window when available, otherwise browser |
+| VS Code terminal | VS Code tab |
+| VS Code remote or tunnel | VS Code tab through a forwarded port |
+| Jupyter or IJulia | Inline iframe |
+| Plain SSH | Browser URL through SSH port forwarding |
+
+For plain SSH, follow [Remote](remote.md#ssh). VS Code tunnel forwarding is
+handled by the extension.
+
+## Cleanup
+
+In Python, close a handle directly or use a context manager:
+
+```python
+handle = arrayview.view(a)
+handle.close()
+
+with arrayview.view(a) as handle:
+    print(handle.url)
+```
+
+`close()` releases that viewer session. Calling it again is a no-op. If cleanup
+fails, it raises an error and can be retried.
+
+## Advanced server setup
+
+Start with `view(A)`. Use a persistent server only for shared or multi-hop
+setups:
+
+```bash
+arrayview --serve
+arrayview data.npy
+```
+
+Use `--relay PORT` only when a reverse SSH tunnel exposes ArrayView on a
+different remote port. See [Remote](remote.md#multi-hop).

{arrayview-0.29.2 → arrayview-0.31.0}/docs/index.md

@@ -26,6 +26,10 @@ view(np.random.rand(256, 256, 32))
 
 Works in scripts, Jupyter notebooks, and VS Code interactive windows.
 
+MATLAB and Julia setup: [MATLAB and Julia](foreign-hosts.md).
+
+Remote and tunnel setup: [Remote](remote.md).
+
 ## Formats
 
 `.npy` `.npz` `.nii` `.nii.gz` `.zarr` `.pt` `.h5` `.tif` `.mat`