driftless-bundle-photometry 0.2.1__py3-none-any.whl

driftless_bundle_photometry-0.2.1.dist-info/METADATA

@@ -0,0 +1,305 @@
+Metadata-Version: 2.5
+Name: driftless-bundle-photometry
+Version: 0.2.1
+Summary: Trace-first multichannel fiber photometry acquisition and NWB recording
+Project-URL: Homepage, https://github.com/mohebi-n-associates/DriftlessBundlePhotometry
+Project-URL: Repository, https://github.com/mohebi-n-associates/DriftlessBundlePhotometry
+Project-URL: Issues, https://github.com/mohebi-n-associates/DriftlessBundlePhotometry/issues
+Project-URL: Changelog, https://github.com/mohebi-n-associates/DriftlessBundlePhotometry/blob/main/WHATS_NEW.md
+Author: Driftless Bundle Photometry contributors
+License: MIT
+License-File: LICENSE
+Keywords: NWB,acquisition,fiber photometry,neuroscience
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Win32 (MS Windows)
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: <3.14,>=3.11
+Requires-Dist: h5py<4,>=3.12
+Requires-Dist: ndx-fiber-photometry<0.3,>=0.2.3
+Requires-Dist: numpy<3,>=2.0
+Requires-Dist: nwbinspector<1,>=0.6
+Requires-Dist: platformdirs<5,>=4.3
+Requires-Dist: pydantic<3,>=2.10
+Requires-Dist: pynwb<5,>=4.0
+Requires-Dist: pyserial<4,>=3.5
+Provides-Extra: dev
+Requires-Dist: pyqtgraph<0.15,>=0.13.7; extra == 'dev'
+Requires-Dist: pyside6<6.9,>=6.8; extra == 'dev'
+Requires-Dist: pytest-cov<7,>=6; extra == 'dev'
+Requires-Dist: pytest-qt<5,>=4.4; extra == 'dev'
+Requires-Dist: pytest<9,>=8.3; extra == 'dev'
+Requires-Dist: ruff<1,>=0.11; extra == 'dev'
+Provides-Extra: gui
+Requires-Dist: pyqtgraph<0.15,>=0.13.7; extra == 'gui'
+Requires-Dist: pyside6<6.9,>=6.8; extra == 'gui'
+Provides-Extra: release
+Requires-Dist: build<2,>=1.2; extra == 'release'
+Requires-Dist: pillow<13,>=11; extra == 'release'
+Requires-Dist: pyinstaller<7,>=6.16; extra == 'release'
+Requires-Dist: twine<8,>=7; extra == 'release'
+Description-Content-Type: text/markdown
+
+# Driftless Bundle Photometry
+
+**Version 0.2.1** · [What's new](WHATS_NEW.md)
+
+A Python-based, trace-first multichannel fiber-photometry acquisition system.
+
+The application supports up to nine circular fiber ROIs, interleaved 405/470/565 nm
+excitation, four edge-recording TTL inputs, optional lossless raw frames, and one
+self-contained NWB-HDF5 output per ROI and animal. Windows is the physical-hardware
+target; the simulator and GUI demo are cross-platform.
+
+## Current implementation
+
+- Immutable validation for sessions, channels, circular ROIs, camera settings, and
+  TTL inputs.
+- Deterministic simulator and a shared headless acquisition engine with explicit
+  lifecycle states.
+- Bounded, checksummed, chunked session spools that survive interruption and disk or
+  finalizer errors.
+- Pre-arm storage-capacity checks and structured live diagnostics for queue pressure,
+  write latency, dropped frames, clock residuals, and NWB finalization stages.
+- Typed acquisition faults are committed as system events and invalid-time markers
+  before an incomplete spool closes whenever committed samples can be recovered.
+- Canonical NWB finalization using PyNWB, `ndx-fiber-photometry`, and
+  `ndx-ophys-devices`, including a separate subject, brain region, sensor type, and
+  validated file for every ROI.
+- Exact per-exposure commanded voltage, controller sequence/tick, camera frame ID,
+  host receipt time, per-ROI saturation QC, explicit excitation events, and marked
+  invalid continuous spans in every independently interpretable animal file.
+- Trace-first PySide6/pyqtgraph desktop demo with a separate calibration image and
+  draggable circular fiber ROIs, plus separate live camera panels for 405, 470, and
+  565 nm exposures.
+- Selectable 15 s, 1 min, 10 min, 1 h, and Full trace horizons with display-only
+  extrema-preserving decimation, keeping long recordings responsive without changing
+  acquired or stored samples.
+- One live plot row per ROI with overlaid 405, 470, and 565 nm traces, independent
+  wavelength visibility controls, and Absolute or display-only dF/F views with a
+  configurable per-ROI/per-wavelength median baseline window.
+- Optional display-only trailing-mean smoothing uses elapsed seconds, works with
+  asynchronously sampled channels, and never changes acquired or stored values.
+- Independent enable/disable controls for each ROI; disabled definitions remain in
+  saved settings but are excluded from extraction, live traces, and NWB output.
+- A required non-writing acquisition preview that validates timing, explicit
+  wavelength coverage, commanded voltages, camera frames, ROI extraction, and
+  saturation before enabling each recording.
+- Synchronized numeric time axes across all ROI rows, horizontal/vertical drag-box
+  zoom, double-click zoom reset, and page scrolling—not graph zoom—under the mouse
+  wheel.
+- Clean numeric entry fields without embedded increment/decrement stepper buttons.
+- Versioned, human-readable JSON settings with GUI actions to save, load, set startup
+  defaults, and restore the complete setup from a previous DBF NWB recording.
+- Settings v2 discriminate the native camera/controller source from the planned RWD
+  read-only bridge and migrate v1 files explicitly to native with a visible warning.
+- A raw uint16 reference frame and fixed-scale ROI-annotated diagnostic view for
+  every wavelength observed in a recording are saved inside each ROI NWB file.
+- Versioned/checksummed controller protocol, fail-safe lifecycle guard, and
+  single-owner serial transport that sends a best-effort `STOP` on close.
+- Lazy Thorlabs SDK detection that does not break simulator mode on macOS.
+
+The CS505MU camera transport, serial controller transport, controller firmware, and
+LED intensity electronics are not yet physically validated. Those require the real
+Windows rig, vendor SDK, trigger cabling, DAC/driver hardware, and bench timing and
+safety measurements. Simulator success is not evidence of physical validation.
+
+The RWD bridge currently has a documented wire contract, validated source settings,
+typed raw domain records, a fixture-tested incremental fluorescence/event parser,
+and a synthetic-data trace-only recovery/NWB path. The RWD spool retains checksummed
+mixed records, exact raw ticks/values and scales, named ON/OFF events, connection
+identity, faults, and invalid spans. Recovery creates one independently validated NWB
+per mapped fiber without inventing camera frames, LED commands, native exposures, or
+numbered TTL inputs. A headless single-owner TCP client now provides bounded
+recording, timeout/disconnect/malformed-stream faults, prompt stop, storage preflight,
+and machine-readable CLI output. The GUI workflow is still being implemented, and
+the desktop setup now begins with a native/simulator or RWD read-only system choice,
+hides camera/LED controls in RWD mode, retains per-fiber animal metadata, and routes
+both sources through the same bounded live-trace presentation contract. Every RWD
+fiber has an explicit device-channel number and an independent operator label. Live
+status reports connection state, decoder counts, spool pressure, committed records,
+and named event activity; raw, elapsed-time-smoothed, and dF/F views remain
+presentation-only.
+The TCP path has only synthetic local-server validation; current builds must not be
+described as a physically validated RWD connection. See
+[the RWD streaming contract](docs/rwd-streaming-protocol.md) and
+[the RWD operator and bench-validation guide](docs/rwd-operator-guide.md).
+
+The historical MATLAB, Arduino, and Bonsai sources remain under `old mescoscope/`
+for reference and are not runtime dependencies.
+
+## Saving and restoring settings
+
+The Configuration panel provides **Save JSON**, **Load JSON**, **Load NWB**, and
+**Set as default**. A settings file includes all session metadata, recording duration,
+output location, native/RWD source selection, source-specific connection settings,
+camera and retention settings, excitation states and voltages, TTL configuration,
+live-display preferences, and every fiber's animal metadata. Settings v1 files are
+accepted only through an explicit migration to the native source because they
+predate system selection.
+
+On Windows, DBF resolves the same Documents folder used by Explorer, including
+OneDrive or other redirected locations, and uses its `Driftless Bundle Photometry`
+folder for settings. **Set as default** writes `default_settings.json` there; DBF
+loads that file automatically at startup. Save and Load dialogs open in the same
+folder by default.
+
+Every newly recorded per-ROI NWB file embeds the complete settings snapshot, so any
+one of those files can restore the whole multi-ROI setup. DBF can also import older
+per-ROI DBF NWBs: it gathers matching sibling files to recover all available ROIs and
+warns when an old file never recorded a setting that must use a safe default.
+Each file also embeds a separate runtime provenance snapshot with the application,
+Python, operating-system, dependency, adapter, and protocol versions that governed
+acquisition or recovery.
+
+## Installation choices
+
+End users on 64-bit Windows should use the standalone installer. Developers should
+use the repository's Conda environment. PyPI is also available for users who already
+manage Python environments. The standalone installer includes Python and all normal
+application dependencies; it does not require Conda or a separate Python install.
+
+### Windows installer for end users
+
+1. Open the [latest GitHub release](https://github.com/mohebi-n-associates/DriftlessBundlePhotometry/releases/latest).
+2. Download `Driftless-Bundle-Photometry-<version>-Windows-x64-Setup.exe`.
+3. Optionally compare its SHA-256 digest with `SHA256SUMS.txt` from the same release.
+4. Run the installer, then launch **Driftless Bundle Photometry** from the Start menu.
+
+The installer is per-user, supports clean uninstall through Windows Settings, and
+does not require administrator access. Current installers are not code-signed, so
+Windows SmartScreen may show an unrecognized-publisher warning. The application can
+run the simulator and RWD read-only path, but the physical Thorlabs/controller path
+must not be treated as validated until the documented Windows bench gates pass.
+
+### Conda environment for developers
+
+Clone the repository and let `environment.yml` create the `dbf` environment plus an
+editable install with GUI, test, lint, build, and release tools:
+
+```bash
+git clone https://github.com/mohebi-n-associates/DriftlessBundlePhotometry.git
+cd DriftlessBundlePhotometry
+conda env create --file environment.yml
+conda activate dbf
+python -m pytest
+```
+
+After pulling dependency changes, synchronize the existing environment with:
+
+```bash
+conda env update --file environment.yml --prune
+```
+
+### PyPI installation
+
+Inside an existing Python 3.11–3.13 environment, install the desktop application
+from PyPI and launch it with:
+
+```bash
+python -m pip install "driftless-bundle-photometry[gui]"
+dbf --version
+dbf --demo
+```
+
+The distribution name is `driftless-bundle-photometry`, the short command and Conda
+environment are `dbf`, and Python imports use `driftless_photometry`. The long
+`driftless-photometry` command remains available. On macOS, use Conda or PyPI for the
+simulator, replay, NWB, analysis, and GUI-demo paths.
+
+## Running developer workflows
+
+Run a headless simulated acquisition:
+
+```bash
+dbf --headless --duration 5 --raw
+```
+
+Run the headless read-only RWD bridge from a validated settings-v2 file:
+
+```bash
+dbf --rwd-settings path/to/rwd.settings.json --duration 60
+```
+
+RWD must already be recording and listening on the host/port stored in that file.
+DBF does not send hardware commands. It makes one connection for one session and
+never reconnects automatically after a fault, because joining records across TCP
+connections could hide a gap or changed device state.
+
+Capture a checksummed exact-wire artifact during a physical bench run, inspect it,
+and replay it unpaced through the production parser/recovery/NWB path:
+
+```bash
+dbf --rwd-settings path/to/rwd.settings.json --duration 300 \
+    --rwd-wire-capture path/to/bench-001.rwd-wire
+dbf --inspect-rwd-capture path/to/bench-001.rwd-wire
+dbf --rwd-settings path/to/replay.settings.json \
+    --rwd-replay path/to/bench-001.rwd-wire
+```
+
+Replay settings must preserve the capture's parsing scales, wavelengths, expected
+machine, and channel/fiber mappings, but should use a new session ID and empty output
+directory. Exact-wire captures can contain experimental data and must not be
+committed to the repository.
+
+Run the GUI demo:
+
+```bash
+dbf --demo
+```
+
+Recover all committed data from a complete or interrupted spool:
+
+```bash
+dbf --recover-spool path/to/session.photometry-spool
+dbf --recover-spool path/to/session.rwd-spool
+```
+
+Inspect direct child spools without creating or removing files:
+
+```bash
+dbf --inspect-spools path/to/output-directory
+```
+
+Inspection recognizes native `*.photometry-spool` and RWD `*.rwd-spool` children,
+verifies checksums, and reports source-specific counts plus completeness, invalid
+times, system events, schema, and output-file count. It deliberately does not recurse
+into unrelated directories. Successful recovery validates the complete
+NWB set before removing the spool; add `--keep-spool` for forensic retention.
+Recovery is idempotent and can resume if a process stopped after validating partials
+or while promoting the multi-ROI set. Existing canonical files must match the spool
+exactly and are never overwritten silently. Incomplete acquisitions are explicitly
+marked in the NWB system event table. Legacy schema-v1 spools remain recoverable, but
+the resulting invalid-time record identifies the per-frame host receipt and commanded
+intensity provenance that those older spools never persisted.
+
+The storage estimate uses configured duration, total frame rate, image dimensions,
+raw-retention policy, enabled ROI count, and a 64 MiB reserve. CI correctness tests
+exercise non-realtime simulator sessions at 300 frames/s trace-only and 60 frames/s
+with raw 32 × 24 frames for one ROI. These small-fixture bounds test queue/data
+integrity; they are not throughput claims for the CS505MU or any physical rig.
+
+Run the release gates:
+
+```bash
+python -m pytest --cov=driftless_photometry --cov-report=term-missing
+python -m ruff check .
+python -m ruff format --check .
+python -m build
+python -m twine check --strict dist/*
+```
+
+The complete release procedure and one-time Trusted Publisher setup are in
+[the release guide](docs/releasing.md).
+
+See [the architecture](docs/architecture.md) and the synchronized agent contracts
+in `AGENTS.md` and `CLAUDE.md`. The planned hardware wire contract is documented in
+[the controller protocol](docs/controller-protocol.md). Development priorities,
+dependencies, and phase exit criteria are maintained in [the roadmap](roadmap.md).

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driftless_bundle_photometry-0.2.1.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: hatchling 1.32.0
+Root-Is-Purelib: true
+Tag: py3-none-any

driftless_bundle_photometry-0.2.1.dist-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+dbf = driftless_photometry.cli:main
+driftless-photometry = driftless_photometry.cli:main

driftless_bundle_photometry-0.2.1.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Driftless Bundle Photometry contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

driftless_photometry/__init__.py

@@ -0,0 +1,10 @@
+"""Driftless Bundle Photometry acquisition package."""
+
+from importlib.metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("driftless-bundle-photometry")
+except PackageNotFoundError:  # pragma: no cover - source tree without installation
+    __version__ = "0+unknown"
+
+__all__ = ["__version__"]

driftless_photometry/__main__.py

@@ -0,0 +1,3 @@
+from driftless_photometry.cli import main
+
+raise SystemExit(main())