mesofield 0.3.2b0__py3-none-any.whl

mesofield-0.3.2b0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: mesofield
+Version: 0.3.2b0
+Summary: Mesofield is an open-source image acquisition Python software package build for the Sipe Laboratory at Pennsylvania State University.
+Author: Jacob Gronemeyer
+License: MIT License
+        
+        Copyright (c) 2024 Gronemeyer
+        
+        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.
+        
+Project-URL: Homepage, https://github.com/Gronemeyer/mesofield/
+Project-URL: Repository, https://github.com/Gronemeyer/mesofield/
+Project-URL: Issues, https://github.com/Gronemeyer/mesofield/issues
+Project-URL: Documentation, https://gronemeyer.github.io/mesofield/
+Keywords: imaging,microscopy,acquisition,neuroscience
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: annotated-types
+Requires-Dist: click
+Requires-Dist: ipykernel
+Requires-Dist: ipython
+Requires-Dist: jupyter_client
+Requires-Dist: jupyter_core
+Requires-Dist: loguru
+Requires-Dist: markdown-it-py
+Requires-Dist: matplotlib
+Requires-Dist: mesokit-schema
+Requires-Dist: nidaqmx
+Requires-Dist: numpy
+Requires-Dist: packaging
+Requires-Dist: pandas
+Requires-Dist: parso
+Requires-Dist: pillow
+Requires-Dist: platformdirs
+Requires-Dist: psygnal
+Requires-Dist: pyaml
+Requires-Dist: opencv-python
+Requires-Dist: pymmcore
+Requires-Dist: pymmcore-plus
+Requires-Dist: pymmcore-widgets
+Requires-Dist: PyQt6
+Requires-Dist: PyQt6-Qt6
+Requires-Dist: PyQt6_sip
+Requires-Dist: pyqtgraph
+Requires-Dist: pyserial
+Requires-Dist: python-dateutil
+Requires-Dist: pytz
+Requires-Dist: pywin32; sys_platform == "win32"
+Requires-Dist: pyzmq
+Requires-Dist: qtconsole
+Requires-Dist: rich
+Requires-Dist: setuptools
+Requires-Dist: tifffile
+Requires-Dist: typer
+Requires-Dist: typer-slim
+Requires-Dist: typing_extensions
+Requires-Dist: useq-schema
+Requires-Dist: wheel
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: coverage; extra == "test"
+Requires-Dist: flake8; extra == "test"
+Requires-Dist: black; extra == "test"
+Requires-Dist: isort; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: mypy; extra == "test"
+Requires-Dist: gitchangelog; extra == "test"
+Provides-Extra: docs
+Requires-Dist: sphinx>=7; extra == "docs"
+Requires-Dist: pydata-sphinx-theme; extra == "docs"
+Requires-Dist: myst-parser; extra == "docs"
+Requires-Dist: sphinx-copybutton; extra == "docs"
+Requires-Dist: sphinx-design; extra == "docs"
+Dynamic: license-file
+
+```
+ __    __     ______     ______     ______     ______   __     ______     __         _____
+/\ "-./  \   /\  ___\   /\  ___\   /\  __ \   /\  ___\ /\ \   /\  ___\   /\ \       /\  __-.
+\ \ \-./\ \  \ \  __\   \ \___  \  \ \ \/\ \  \ \  __\ \ \ \  \ \  __\   \ \ \____  \ \ \/\ \
+ \ \_\ \ \_\  \ \_____\  \/\_____\  \ \_____\  \ \_\    \ \_\  \ \_____\  \ \_____\  \ \____-
+  \/_/  \/_/   \/_____/   \/_____/   \/_____/   \/_/     \/_/   \/_____/   \/_____/   \/____/
+```
+
+Mesofield is a PyQt6-based framework for running real-time, multi-camera
+neuroscience experiments. It coordinates hardware via serial connections
+and MicroManager (through [pymmcore-plus](https://pymmcore-plus.github.io/pymmcore-plus/)
+custom `MDAEngine`s and multi-`CMMCorePlus` instancing) and manages
+experiment configuration, acquisition orchestration, and data logging.
+The project is aimed at laboratory use and is not a full production
+package; some specialised knowledge of device hardware and
+MicroManager device configuration is necessary to get started.
+
+<img width="2454" height="1592" alt="Mesofield acquisition window" src="https://github.com/user-attachments/assets/151196ab-2d74-4644-85b7-c4facf3b779a" />
+
+---
+
+## Documentation
+
+Documentation lives at **[gronemeyer.github.io/mesofield](https://gronemeyer.github.io/mesofield/)**
+and is split by audience:
+
+- **[Tutorial](https://gronemeyer.github.io/mesofield/tutorial.html)** —
+  the fastest path from a fresh conda env to a working acquisition on
+  your hardware.
+- **[User Guide](https://gronemeyer.github.io/mesofield/user_guide.html)** —
+  for experimenters running acquisitions: launching the GUI, writing
+  `experiment.json`, interpreting the on-disk output.
+- **[Developer Guide](https://gronemeyer.github.io/mesofield/developer_guide.html)** —
+  for developers extending mesofield: custom devices, `Procedure`
+  subclasses, frame processors, threading models.
+- **[API Reference](https://gronemeyer.github.io/mesofield/api/index.html)** —
+  auto-generated from docstrings.
+
+---
+
+## Quick start
+
+```bash
+conda create -n mesofield python=3.12 -y
+conda activate mesofield
+pip install -e .
+```
+
+Launch an acquisition:
+
+```bash
+mesofield launch path/to/experiment.json
+```
+
+Scaffold a new experiment:
+
+```bash
+mesofield new my-experiment
+```
+
+For end-to-end setup, follow the
+[Tutorial](https://gronemeyer.github.io/mesofield/tutorial.html).
+
+---
+
+## System requirements
+
+Tested on Windows 10/11. For multi-camera acquisition with large files
+we recommend ≥ 32 GB RAM, a 12th-gen Intel i7 or equivalent, and fast
+local NVMe storage for the experiment directory.
+
+---
+
+## License
+
+MIT — see `LICENSE`.

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+mesofield-0.3.2b0.dist-info/METADATA,sha256=Uy99aQ_JFvWN32rkaLlU46uEXTJODicxFSa0xEgeFKQ,6653
+mesofield-0.3.2b0.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
+mesofield-0.3.2b0.dist-info/entry_points.txt,sha256=nDsPDlUztjAGQC1awrNrSC4tnrxbpNYd4uL2lrfTc0s,48
+mesofield-0.3.2b0.dist-info/top_level.txt,sha256=t_c9i9mTQRzaM345eXWVMqlGjyKXZgG23RYVPhZg0oU,53
+mesofield-0.3.2b0.dist-info/RECORD,,

mesofield-0.3.2b0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (82.0.1)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

mesofield-0.3.2b0.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+mesofield = mesofield.cli:cli

mesofield-0.3.2b0.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Gronemeyer
+
+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.

mesofield-0.3.2b0.dist-info/top_level.txt

@@ -0,0 +1,6 @@
+docs
+examples
+experiments
+external
+mesofield
+scripts

scripts/bench_frame_processor.py

@@ -0,0 +1,103 @@
+"""Stress harness for :class:`mesofield.processors.FrameProcessor`.
+
+Emits synthetic frames through ``DeviceSignals.frame`` at a target rate
+with a configurable image size and (optional) artificial compute load,
+then prints throughput, drop %, and EWMA / max compute time.
+
+No real camera or Qt is required.  Example::
+
+    python scripts/bench_frame_processor.py --size 512 --fps 60 --seconds 3
+    python scripts/bench_frame_processor.py --size 2048 --fps 120 \\
+        --extra-compute-ms 5 --seconds 5
+"""
+
+from __future__ import annotations
+
+import argparse
+import time
+from typing import Any, Optional
+
+import numpy as np
+
+from mesofield.processors import FrameMean
+from mesofield.signals import DeviceSignals
+
+
+class _FakeCamera:
+    def __init__(self, fps: float) -> None:
+        self.signals = DeviceSignals()
+        self.sampling_rate = fps
+
+
+class _BenchMean(FrameMean):
+    """FrameMean with an optional artificial compute delay."""
+
+    def __init__(self, *args: Any, extra_compute_ms: float = 0.0, **kw: Any) -> None:
+        super().__init__(*args, **kw)
+        self._extra_s = extra_compute_ms / 1000.0
+
+    def compute(self, img: Any, idx: Any, ts: Any) -> Optional[float]:
+        v = super().compute(img, idx, ts)
+        if self._extra_s > 0:
+            time.sleep(self._extra_s)
+        return v
+
+
+def run(size: int, fps: float, seconds: float, extra_compute_ms: float) -> dict:
+    cam = _FakeCamera(fps=fps)
+    proc = _BenchMean(name="bench", camera=cam, extra_compute_ms=extra_compute_ms)
+    proc.attach(cam)
+
+    period = 1.0 / fps if fps > 0 else 0.0
+    n_target = int(seconds * fps)
+    img_buf = np.random.default_rng(0).integers(
+        0, 255, size=(size, size), dtype=np.uint16
+    )
+
+    emit_t0 = time.perf_counter()
+    next_t = emit_t0
+    for i in range(n_target):
+        # Mutate a couple of pixels so the mean changes each frame.
+        img_buf[i % size, 0] = (i * 13) & 0xFF
+        cam.signals.frame.emit(img_buf, i, time.perf_counter() - emit_t0)
+        if period:
+            next_t += period
+            sleep_for = next_t - time.perf_counter()
+            if sleep_for > 0:
+                time.sleep(sleep_for)
+    emit_elapsed = time.perf_counter() - emit_t0
+
+    # Let the worker drain the last frame.
+    time.sleep(max(0.1, (proc.compute_ms_ewma * 3) / 1000.0))
+    proc.detach()
+
+    s = proc.status()
+    s["emit_elapsed_s"] = round(emit_elapsed, 3)
+    s["target_fps"] = fps
+    s["actual_emit_fps"] = round(n_target / emit_elapsed, 1) if emit_elapsed else 0.0
+    s["frame_size"] = f"{size}x{size}"
+    s["extra_compute_ms"] = extra_compute_ms
+    return s
+
+
+def main() -> None:
+    p = argparse.ArgumentParser()
+    p.add_argument("--size", type=int, default=512, help="square frame edge (px)")
+    p.add_argument("--fps", type=float, default=60.0, help="target emission rate")
+    p.add_argument("--seconds", type=float, default=3.0, help="run duration")
+    p.add_argument(
+        "--extra-compute-ms",
+        type=float,
+        default=0.0,
+        help="extra artificial compute load per frame (ms)",
+    )
+    args = p.parse_args()
+
+    s = run(args.size, args.fps, args.seconds, args.extra_compute_ms)
+    width = max(len(k) for k in s)
+    for k, v in s.items():
+        print(f"  {k:<{width}} : {v}")
+
+
+if __name__ == "__main__":
+    main()