neuralib-parser 0.7.0__tar.gz

neuralib_parser-0.7.0/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2023, YT.WEI
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

neuralib_parser-0.7.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: neuralib-parser
+Version: 0.7.0
+Summary: Parsers for output from open-source packages or specific devices
+Author-email: Yu-Ting Wei <ytsimon2004@gmail.com>, Ta-Shun Su <antoniost29@gmail.com>
+License: BSD-3-Clause
+Project-URL: Homepage, https://github.com/ytsimon2004/neuralib2
+Project-URL: Documentation, https://neuralib2.readthedocs.io/en/latest/index.html
+Project-URL: Repository, https://github.com/ytsimon2004/neuralib2
+Project-URL: Issues, https://github.com/ytsimon2004/neuralib2/issues
+Keywords: Parser,Segmentation,Morphology
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Natural Language :: English
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering
+Classifier: Intended Audience :: Science/Research
+Classifier: Typing :: Typed
+Requires-Python: <3.13,>=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: neuralib-utils[all]>=0.7.0
+Requires-Dist: numpy
+Provides-Extra: stardist
+Requires-Dist: stardist; extra == "stardist"
+Requires-Dist: roifile; extra == "stardist"
+Requires-Dist: tensorflow; extra == "stardist"
+Requires-Dist: numpy<2.0; extra == "stardist" and extra == "stardist"
+Requires-Dist: napari; extra == "stardist"
+Provides-Extra: suite2p
+Requires-Dist: neuralib-imaging>=0.7.0; extra == "suite2p"
+Provides-Extra: czi
+Requires-Dist: aicspylibczi; extra == "czi"
+Requires-Dist: xmltodict; extra == "czi"
+Provides-Extra: sbx
+Requires-Dist: sbxreader; extra == "sbx"
+Provides-Extra: all
+Requires-Dist: neuralib-parser[suite2p]; extra == "all"
+Requires-Dist: neuralib-parser[sbx]; extra == "all"
+Requires-Dist: tifffile; extra == "all"
+Dynamic: license-file
+
+# neuralib-parser
+
+Data parsers for neuroscience research tools and file formats, providing unified interfaces for segmentation,
+morphology, imaging, tracking, and confocal microscopy data.
+
+## Overview
+
+`neuralib-parser` provides Python parsers and data structures for output from open-source packages and specific imaging
+devices. It includes:
+
+- **Segmentation**: Cellpose, StarDist cell segmentation
+- **Morphology**: SWC neuron morphology files
+- **Imaging**: Suite2p, Scanbox data formats
+- **Tracking**: DeepLabCut, Facemap behavioral tracking
+- **Confocal Scans**: Zeiss CZI, LSM file formats
+
+
+## Installation
+
+### From PyPI
+
+```bash
+pip install neuralib-parser
+```
+
+### With Optional Dependencies
+
+```bash
+# StarDist support (requires numpy<2.0)
+pip install neuralib-parser[stardist]
+
+# Suite2p integration
+pip install neuralib-parser[suite2p]
+
+# Zeiss CZI format support
+pip install neuralib-parser[czi]
+
+# Scanbox reader
+pip install neuralib-parser[sbx]
+
+# All features (excludes stardist due to numpy<2.0 constraint)
+pip install neuralib-parser[all]
+```
+
+### From Source (uv recommended)
+
+```bash
+git clone https://github.com/ytsimon2004/neuralib2.git
+cd neuralib2/packages/neuralib-parser
+uv pip install -e .        # Basic installation
+uv pip install -e ".[all]" # With optional features
+```
+
+### Requirements
+
+- Python 3.11 or 3.12
+- Core dependencies: `neuralib-utils`, `numpy`
+- See `pyproject.toml` for optional dependencies
+
+## Documentation
+
+- **Main Documentation**: [https://neuralib2.readthedocs.io/](https://neuralib2.readthedocs.io/en/latest/index.html)
+- **GitHub Repository**: [https://github.com/ytsimon2004/neuralib2](https://github.com/ytsimon2004/neuralib2)
+- **Issue Tracker**: [https://github.com/ytsimon2004/neuralib2/issues](https://github.com/ytsimon2004/neuralib2/issues)
+
+## Important Notes
+
+### StarDist and NumPy 2.0
+
+StarDist requires `numpy<2.0` due to upstream compatibility. The `stardist` extra explicitly pins this constraint:
+
+## License
+
+BSD 3-Clause License. See LICENSE file for details.
+
+## Contributing
+
+Contributions are welcome! Please:
+
+1. Fork the repository
+2. Create a feature branch
+3. Submit a pull request with clear description
+
+For bug reports and feature requests, use the [GitHub issue tracker](https://github.com/ytsimon2004/neuralib2/issues).
+
+## Acknowledgments
+
+This package provides interfaces to:
+
+- [Suite2p](https://github.com/MouseLand/suite2p) - Calcium imaging data analysis
+- [Scanbox](http://scanbox.org/) - Two-photon imaging system
+- [StarDist](https://github.com/stardist/stardist) - Cell segmentation
+- [Cellpose](https://github.com/MouseLand/cellpose) - Cell segmentation
+- [DeepLabCut](https://github.com/DeepLabCut/DeepLabCut) - Pose estimation
+- [Facemap](https://github.com/MouseLand/facemap) - Behavioral video analysis

neuralib_parser-0.7.0/README.md

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+# neuralib-parser
+
+Data parsers for neuroscience research tools and file formats, providing unified interfaces for segmentation,
+morphology, imaging, tracking, and confocal microscopy data.
+
+## Overview
+
+`neuralib-parser` provides Python parsers and data structures for output from open-source packages and specific imaging
+devices. It includes:
+
+- **Segmentation**: Cellpose, StarDist cell segmentation
+- **Morphology**: SWC neuron morphology files
+- **Imaging**: Suite2p, Scanbox data formats
+- **Tracking**: DeepLabCut, Facemap behavioral tracking
+- **Confocal Scans**: Zeiss CZI, LSM file formats
+
+
+## Installation
+
+### From PyPI
+
+```bash
+pip install neuralib-parser
+```
+
+### With Optional Dependencies
+
+```bash
+# StarDist support (requires numpy<2.0)
+pip install neuralib-parser[stardist]
+
+# Suite2p integration
+pip install neuralib-parser[suite2p]
+
+# Zeiss CZI format support
+pip install neuralib-parser[czi]
+
+# Scanbox reader
+pip install neuralib-parser[sbx]
+
+# All features (excludes stardist due to numpy<2.0 constraint)
+pip install neuralib-parser[all]
+```
+
+### From Source (uv recommended)
+
+```bash
+git clone https://github.com/ytsimon2004/neuralib2.git
+cd neuralib2/packages/neuralib-parser
+uv pip install -e .        # Basic installation
+uv pip install -e ".[all]" # With optional features
+```
+
+### Requirements
+
+- Python 3.11 or 3.12
+- Core dependencies: `neuralib-utils`, `numpy`
+- See `pyproject.toml` for optional dependencies
+
+## Documentation
+
+- **Main Documentation**: [https://neuralib2.readthedocs.io/](https://neuralib2.readthedocs.io/en/latest/index.html)
+- **GitHub Repository**: [https://github.com/ytsimon2004/neuralib2](https://github.com/ytsimon2004/neuralib2)
+- **Issue Tracker**: [https://github.com/ytsimon2004/neuralib2/issues](https://github.com/ytsimon2004/neuralib2/issues)
+
+## Important Notes
+
+### StarDist and NumPy 2.0
+
+StarDist requires `numpy<2.0` due to upstream compatibility. The `stardist` extra explicitly pins this constraint:
+
+## License
+
+BSD 3-Clause License. See LICENSE file for details.
+
+## Contributing
+
+Contributions are welcome! Please:
+
+1. Fork the repository
+2. Create a feature branch
+3. Submit a pull request with clear description
+
+For bug reports and feature requests, use the [GitHub issue tracker](https://github.com/ytsimon2004/neuralib2/issues).
+
+## Acknowledgments
+
+This package provides interfaces to:
+
+- [Suite2p](https://github.com/MouseLand/suite2p) - Calcium imaging data analysis
+- [Scanbox](http://scanbox.org/) - Two-photon imaging system
+- [StarDist](https://github.com/stardist/stardist) - Cell segmentation
+- [Cellpose](https://github.com/MouseLand/cellpose) - Cell segmentation
+- [DeepLabCut](https://github.com/DeepLabCut/DeepLabCut) - Pose estimation
+- [Facemap](https://github.com/MouseLand/facemap) - Behavioral video analysis

neuralib_parser-0.7.0/pyproject.toml

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+[project]
+name = "neuralib-parser"
+version = "0.7.0"
+requires-python = ">=3.11,<3.13"
+description = "Parsers for output from open-source packages or specific devices"
+authors = [
+    { name = "Yu-Ting Wei", email = "ytsimon2004@gmail.com" },
+    { name = "Ta-Shun Su", email = "antoniost29@gmail.com" }
+]
+license = { text = "BSD-3-Clause" }
+readme = "README.md"
+keywords = ["Parser", "Segmentation", "Morphology"]
+classifiers = [
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "License :: OSI Approved :: BSD License",
+    "Natural Language :: English",
+    "Operating System :: OS Independent",
+    "Topic :: Scientific/Engineering",
+    'Intended Audience :: Science/Research',
+    "Typing :: Typed",
+]
+
+dependencies = [
+    "neuralib-utils[all]>=0.7.0",
+    "numpy",
+]
+
+[project.optional-dependencies]
+
+stardist = ["stardist", "roifile", "tensorflow", "numpy<2.0; extra == 'stardist'", "napari"]
+suite2p = ["neuralib-imaging>=0.7.0"]
+czi = ["aicspylibczi", "xmltodict"]
+sbx = ["sbxreader"]
+
+all = [
+    "neuralib-parser[suite2p]",
+    "neuralib-parser[sbx]",
+    "tifffile"
+]
+
+[project.urls]
+Homepage = "https://github.com/ytsimon2004/neuralib2"
+Documentation = "https://neuralib2.readthedocs.io/en/latest/index.html"
+Repository = "https://github.com/ytsimon2004/neuralib2"
+Issues = "https://github.com/ytsimon2004/neuralib2/issues"
+
+[build-system]
+build-backend = "setuptools.build_meta"
+requires = ["setuptools>=61.0"]
+
+[tool.setuptools.packages.find]
+where = ["src"]

neuralib_parser-0.7.0/setup.cfg

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

neuralib_parser-0.7.0/src/neuralib/cellpose/__init__.py

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+from .core import *

neuralib_parser-0.7.0/src/neuralib/cellpose/core.py

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+from __future__ import annotations
+
+from pathlib import Path
+
+import numpy as np
+from typing import Self
+
+from neuralib.typing import PathLike
+
+__all__ = [
+    'read_cellpose',
+    'cellpose_point_roi_helper',
+    'CellposeSegmentation'
+]
+
+
+def read_cellpose(file: PathLike) -> CellposeSegmentation:
+    """
+    Read a cellpose segmentation result file
+
+    :param file: cellpose segmentation result ``.npy`` file
+    :return: :class:`CellposeSegmentation`
+    """
+    return CellposeSegmentation.load(file)
+
+
+def cellpose_point_roi_helper(file: PathLike, output: PathLike) -> None:
+    """
+    Read a cellpose segmentation result and convert the segmentation result to point coordinates
+
+    :param file: cellpose segmentation result ``.npy`` file
+    :param output: ``*.roi`` output file path
+    """
+    CellposeSegmentation.load(file).to_roi(output)
+
+
+class CellposeSegmentation:
+    """`Cellpose <https://github.com/MouseLand/cellpose>`_ segmentation results
+
+    `Dimension parameters`:
+
+        N = Number of segmented cells
+
+        W = Image width
+
+        H = Image height
+
+    .. seealso::
+
+        `Cellpose Native Doc <https://cellpose.readthedocs.io/en/latest/outputs.html#seg-npy-output>`_
+
+    """
+
+    def __init__(self, outlines, masks, chan_choose, ismanual, flows, diameter, filename):
+        self._outlines = outlines
+        self._masks = masks
+        self._chan_choose = chan_choose
+        self._is_manual = ismanual
+        self._flows = flows
+        self._diameter = diameter
+
+        self._filename = filename
+
+    @classmethod
+    def load(cls, file: PathLike) -> Self:
+        """
+        Load a cellpose segmentation result
+
+        :param file: cellpose segmentation result ``.npy`` file
+        :return: :class:`CellposeSegmentation`
+        """
+        dat = np.load(file, allow_pickle=True).item()
+        return cls(**dat)
+
+    @property
+    def n_segmentation(self) -> int:
+        """number of segmented cells"""
+        return len(self._is_manual)
+
+    @property
+    def width(self):
+        """image width"""
+        return self._outlines.shape[1]
+
+    @property
+    def height(self):
+        """image height"""
+        return self._outlines.shape[0]
+
+    @property
+    def filename(self) -> Path:
+        """filepath of image"""
+        return Path(self._filename)
+
+    @property
+    def outlines(self) -> np.ndarray:
+        """outlines of ROIs (0 = NO outline; 1,2,… = outline labels). `Array[uint16, [H, W]]`"""
+        return self._outlines
+
+    @property
+    def masks(self) -> np.ndarray:
+        """each pixel in the image is assigned to an ROI (0 = NO ROI; 1,2,… = ROI labels). `Array[uint16, [H, W]]` """
+        return self._masks
+
+    @property
+    def chan_choose(self) -> list[int]:
+        """channels that you chose in GUI (0=gray/none, 1=red, 2=green, 3=blue)"""
+        return self._chan_choose
+
+    @property
+    def flows(self) -> list[np.ndarray]:
+        """
+        flows[0] is XY flow in RGB
+
+        flows[1] is the cell probability in range 0-255 instead of -10.0 to 10.0
+
+        flows[2] is Z flow in range 0-255 (if it exists, otherwise zeros),
+
+        flows[3] is [dY, dX, cellprob] (or [dZ, dY, dX, cellprob] for 3D), flows[4] is pixel destinations (for internal use)
+        """
+        return self._flows
+
+    @property
+    def diameter(self) -> float:
+        """cell body diameter"""
+        return self._diameter
+
+    @property
+    def is_manual(self) -> np.ndarray:
+        """whether or not mask k was manually drawn or computed by the cellpose algorithm. `Array[bool, N]`"""
+        return self._is_manual
+
+    @property
+    def nan_masks(self) -> np.ndarray:
+        """value 0 in :attr:`CellposeSegmentation.masks` to nan"""
+        masks = self.masks.copy().astype(np.float_)
+        masks[masks == 0] = np.nan
+
+        return masks
+
+    @property
+    def nan_outlines(self) -> np.ndarray:
+        """value 0 in :attr:`CellposeSegmentation.outlines` to nan"""
+        outlines = self.outlines.copy().astype(np.float_)
+        outlines[outlines == 0] = np.nan
+
+        return outlines
+
+    @property
+    def points(self) -> np.ndarray:
+        """Calculate center of each segmented area in XY pixel. `Array[int, [N, 2]]`"""
+        centers = self._calculate_centers()
+        return np.round(centers).astype(int)
+
+    # noinspection PyTypeChecker
+    def to_roi(self, output_file: PathLike):
+        """
+        Covert segmented roi to point roi, and save it as ``.roi`` for imageJ.
+
+        :param output_file: ``*.roi`` output file path
+        """
+        from roifile import ImagejRoi, ROI_TYPE, ROI_OPTIONS
+
+        if Path(output_file).suffix != '.roi':
+            raise ValueError('output file must have .roi extension')
+
+        points = np.fliplr(self.points)  # XY rotate in .roi format
+        roi = ImagejRoi(
+            roitype=ROI_TYPE.POINT,
+            options=ROI_OPTIONS.PROMPT_BEFORE_DELETING | ROI_OPTIONS.SUB_PIXEL_RESOLUTION,
+            n_coordinates=self.points.shape[0],
+            integer_coordinates=points,
+            subpixel_coordinates=points
+        )
+
+        roi.tofile(output_file)
+
+    def _calculate_centers(self):
+        """calculate center of each segmented area in XY pixel"""
+        labels = np.unique(self.masks)
+        labels = labels[labels != 0]  # remove background
+
+        n_neurons = len(labels)
+        centers = np.zeros((n_neurons, 2))
+        for i, label in enumerate(labels):
+            segment_coords = np.argwhere(self.masks == label)
+            center = segment_coords.mean(axis=0)
+            centers[i] = center
+
+        return centers

neuralib_parser-0.7.0/src/neuralib/deeplabcut/__init__.py

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+from .core import *