torch-volpy 0.1.0__tar.gz

torch_volpy-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 bobqianic
+
+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.

torch_volpy-0.1.0/MANIFEST.in

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+include README.md
+include LICENSE
+include pyproject.toml
+
+prune .idea
+prune .venv
+prune _test
+prune build
+prune dist
+
+global-exclude __pycache__
+global-exclude *.py[cod]
+global-exclude *.pyo
+global-exclude *.h5
+global-exclude *.hdf5
+global-exclude *.tif
+global-exclude *.tiff
+global-exclude *.pt
+global-exclude *.npy
+global-exclude *.mat
+global-exclude *.png

torch_volpy-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: torch-volpy
+Version: 0.1.0
+Summary: PyTorch tools for voltage imaging movie processing and signal extraction.
+License-Expression: MIT
+Keywords: voltage-imaging,calcium-imaging,neuroscience,pytorch,signal-extraction,motion-correction
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: cellpose
+Requires-Dist: h5py>=3.8
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: numpy>=1.24
+Requires-Dist: tifffile>=2023.7.10
+Requires-Dist: torch>=2.0
+Provides-Extra: segmentation
+Provides-Extra: gui
+Requires-Dist: PyQt6>=6.6; extra == "gui"
+Provides-Extra: dev
+Requires-Dist: build>=1.2; extra == "dev"
+Requires-Dist: pytest>=8; extra == "dev"
+Requires-Dist: twine>=5; extra == "dev"
+Dynamic: license-file
+
+# torch-volpy
+
+PyTorch tools for voltage imaging movie processing and signal extraction.
+
+The package currently provides:
+
+- HDF5-backed movie I/O through `Movie`
+- Motion template building, translation estimation, and motion correction
+- Gaussian high-pass filtering
+- Summary image generation
+- Cellpose-based segmentation support
+- ALI and SpikePursuit signal extraction
+
+## Installation
+
+```bash
+pip install torch-volpy
+```
+
+Install the GUI extra for interactive movie viewing and ROI trace extraction:
+
+```bash
+pip install "torch-volpy[gui]"
+torch-volpy-gui
+```
+
+For local development from this repository:
+
+```bash
+python -m pip install -e ".[gui,dev]"
+```
+
+## Basic Imports
+
+```python
+from torch_volpy.movie import Movie
+from torch_volpy.motion import MotionCorrect, Template, Translation
+from torch_volpy.filter import Filter
+from torch_volpy.model import Summary
+from torch_volpy.extraction import ALI, Spikepursuit
+from torch_volpy.model import Cellpose
+```
+
+## GUI
+
+The PyQt GUI opens HDF5 movies (`.h5`/`.hdf5`, dataset defaults to `movie`) and
+TIFF stacks (`.tif`/`.tiff`). It provides frame playback, Cellpose ROI
+generation from a summary image, loading existing ROI masks (`.tif`, `.npy`,
+`.npz`, `.h5`/`.hdf5`), click-to-select ROI picking, and trace extraction with:
+
+- `Spikepursuit` as the default extraction method
+- `ALI` for cropped ROI activity localization
+- a simple mean-ROI trace for quick inspection
+
+The Cellpose ROI button follows the test workflow in `_test/test_cellpose.py`:
+build `Summary(movie)`, stack `[mean, mean, corr]`, and pass that image to
+`Cellpose.build(...)`. The resulting labeled mask is shown as an overlay; click
+an ROI in `Select` mode to choose which label is used for trace extraction.
+
+When opening a TIFF stack, the GUI first converts it to a sibling HDF5 file,
+runs motion correction into `corrected_<name>.h5`, and then displays the
+corrected HDF5 movie. A progress bar in the Movie panel reports conversion and
+motion-correction phases.
+
+<p align="center">
+  <img src="./media/2026-06-06%20231838.png" width="800" alt="App Screenshot">
+</p>
+<p align="center">
+  <img src="./media/2026-06-06%20232535.png" width="800" alt="App Screenshot">
+</p>
+
+## How To Build
+
+```bash
+python -m build
+```
+
+The build artifacts are written to `dist/`.

torch_volpy-0.1.0/README.md

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+# torch-volpy
+
+PyTorch tools for voltage imaging movie processing and signal extraction.
+
+The package currently provides:
+
+- HDF5-backed movie I/O through `Movie`
+- Motion template building, translation estimation, and motion correction
+- Gaussian high-pass filtering
+- Summary image generation
+- Cellpose-based segmentation support
+- ALI and SpikePursuit signal extraction
+
+## Installation
+
+```bash
+pip install torch-volpy
+```
+
+Install the GUI extra for interactive movie viewing and ROI trace extraction:
+
+```bash
+pip install "torch-volpy[gui]"
+torch-volpy-gui
+```
+
+For local development from this repository:
+
+```bash
+python -m pip install -e ".[gui,dev]"
+```
+
+## Basic Imports
+
+```python
+from torch_volpy.movie import Movie
+from torch_volpy.motion import MotionCorrect, Template, Translation
+from torch_volpy.filter import Filter
+from torch_volpy.model import Summary
+from torch_volpy.extraction import ALI, Spikepursuit
+from torch_volpy.model import Cellpose
+```
+
+## GUI
+
+The PyQt GUI opens HDF5 movies (`.h5`/`.hdf5`, dataset defaults to `movie`) and
+TIFF stacks (`.tif`/`.tiff`). It provides frame playback, Cellpose ROI
+generation from a summary image, loading existing ROI masks (`.tif`, `.npy`,
+`.npz`, `.h5`/`.hdf5`), click-to-select ROI picking, and trace extraction with:
+
+- `Spikepursuit` as the default extraction method
+- `ALI` for cropped ROI activity localization
+- a simple mean-ROI trace for quick inspection
+
+The Cellpose ROI button follows the test workflow in `_test/test_cellpose.py`:
+build `Summary(movie)`, stack `[mean, mean, corr]`, and pass that image to
+`Cellpose.build(...)`. The resulting labeled mask is shown as an overlay; click
+an ROI in `Select` mode to choose which label is used for trace extraction.
+
+When opening a TIFF stack, the GUI first converts it to a sibling HDF5 file,
+runs motion correction into `corrected_<name>.h5`, and then displays the
+corrected HDF5 movie. A progress bar in the Movie panel reports conversion and
+motion-correction phases.
+
+<p align="center">
+  <img src="./media/2026-06-06%20231838.png" width="800" alt="App Screenshot">
+</p>
+<p align="center">
+  <img src="./media/2026-06-06%20232535.png" width="800" alt="App Screenshot">
+</p>
+
+## How To Build
+
+```bash
+python -m build
+```
+
+The build artifacts are written to `dist/`.

torch_volpy-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=69", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "torch-volpy"
+version = "0.1.0"
+description = "PyTorch tools for voltage imaging movie processing and signal extraction."
+readme = "README.md"
+license = "MIT"
+requires-python = ">=3.10"
+keywords = [
+    "voltage-imaging",
+    "calcium-imaging",
+    "neuroscience",
+    "pytorch",
+    "signal-extraction",
+    "motion-correction",
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Image Processing",
+]
+dependencies = [
+    "cellpose",
+    "h5py>=3.8",
+    "matplotlib>=3.7",
+    "numpy>=1.24",
+    "tifffile>=2023.7.10",
+    "torch>=2.0",
+]
+
+[project.optional-dependencies]
+segmentation = []
+gui = [
+    "PyQt6>=6.6",
+]
+dev = [
+    "build>=1.2",
+    "pytest>=8",
+    "twine>=5",
+]
+
+[project.scripts]
+torch-volpy-gui = "torch_volpy.gui.qt_app:main"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["torch_volpy*"]
+
+[tool.setuptools.package-data]
+torch_volpy = ["gui/assets/*.svg"]

torch_volpy-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

torch_volpy-0.1.0/src/torch_volpy/__init__.py

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+"""PyTorch tools for voltage imaging movie processing and signal extraction."""
+
+from importlib.metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("torch-volpy")
+except PackageNotFoundError:
+    __version__ = "0.0.0"
+
+__all__ = ["__version__"]