lbm_suite2p_python 1.0.2__tar.gz

lbm_suite2p_python-1.0.2/LICENSE.md

@@ -0,0 +1,38 @@
+This software license is the 3-clause BSD license plus a fourth clause that 
+prohibits redistribution for commercial purposes without further permission.
+
+BSD 3-Clause License
+
+Copyright (c) 2024, Miller Brain Observatory.
+
+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.
+   
+4. Redistributions for commercial purposes are not permitted without the
+   written permission of the code owner Kushal Kolar.
+   For purposes of this license, commercial purposes is the incorporation of 
+   mesmerize-core into anything for which you will charge fees or other 
+   compensation. Contact kushalkolar@alumni.ubc.ca for more information.
+
+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.
+

lbm_suite2p_python-1.0.2/MANIFEST.in

@@ -0,0 +1 @@
+exclude data/*

lbm_suite2p_python-1.0.2/PKG-INFO

@@ -0,0 +1,78 @@
+Metadata-Version: 2.4
+Name: lbm_suite2p_python
+Version: 1.0.2
+Summary: Light Beads Microscopy Pipeline using Suite2p
+License-Expression: BSD-3-Clause
+Project-URL: homepage, https://github.com/MillerBrainObservatory/LBM-Suite2p-Python
+Keywords: Pipeline,Numpy,Microscopy,ScanImage,Suite2p,tiff
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3 :: Only
+Requires-Python: <3.13,>=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: tifffile>=2025.3.30
+Requires-Dist: zarr>=2.18.3
+Requires-Dist: dask>=2025.3.0
+Requires-Dist: mkl-fft>=1.3.13
+Requires-Dist: imageio[ffmpeg]
+Requires-Dist: matplotlib>=3.10.1
+Requires-Dist: h5py
+Requires-Dist: tqdm
+Requires-Dist: mbo_utilities[all]
+Requires-Dist: suite2p_mbo<2.0.0,>=1.0.0
+Provides-Extra: napari
+Requires-Dist: napari; extra == "napari"
+Provides-Extra: all
+Requires-Dist: napari; extra == "all"
+Dynamic: license-file
+
+# Light Beads Microscopy (LBM) Pipeline: Suite2p
+
+[![PyPI - Version](https://img.shields.io/pypi/v/lbm-suite2p-python)](https://pypi.org/project/lbm-suite2p-python/)
+
+[![Documentation](https://img.shields.io/badge/Documentation-blue?style=for-the-badge&logo=readthedocs&logoColor=white)](https://millerbrainobservatory.github.io/LBM-Suite2p-Python/index.html)
+
+This package is still in a *beta* stage of development.
+
+A pipeline for processing 2-photon Light Beads Microscopy (LBM) datasets.
+
+This pipeline uses the following software:
+
+- [suite2p](https://github.com/MouseLand/suite2p)
+- [cellpose](https://github.com/MouseLand/cellpose)
+- [rastermap](https://github.com/MouseLand/rastermap)
+- [mbo_utilities](https://github.com/MillerBrainObservatory/mbo_utilities)
+- [scanreader](https://github.com/atlab/scanreader)
+
+
+[![LBM](https://zenodo.org/badge/DOI/10.1007/978-3-319-76207-4_15.svg)](https://doi.org/10.1038/s41592-021-01239-8)
+
+---
+
+## Installation
+
+See the [installation documentation](https://millerbrainobservatory.github.io/LBM-Suite2p-Python/install.html) for more details.
+
+This pipeline is fully installable with `pip`.
+
+`conda` can still be used for the virual environment, but be mindful to only install packages with `conda install` when absolutely necessary.
+
+We recommend cloning the repository, until a more established workflow is available to upload to PyPi.
+
+```
+git clone https://github.com/MillerBrainObservatory/LBM-Suite2p-Python.git
+git clone https://github.com/Suite3D # TODO
+cd LBM-Suite2p-Python
+
+# make sure your virtual environment is active
+pip install ".[all]"  # optional, contains ".[gui, notebook]"
+```
+
+---
+
+## Acknowledgements
+
+Thank you to the developers of [scanreader](https://github.com/atlab/scanreader), which provides a clean interface to ScanImage metadata using only tifffile and numpy.
+
+We vendor this repository because it is not published to an indexable Python package registry like PyPI.

lbm_suite2p_python-1.0.2/README.md

@@ -0,0 +1,49 @@
+# Light Beads Microscopy (LBM) Pipeline: Suite2p
+
+[![PyPI - Version](https://img.shields.io/pypi/v/lbm-suite2p-python)](https://pypi.org/project/lbm-suite2p-python/)
+
+[![Documentation](https://img.shields.io/badge/Documentation-blue?style=for-the-badge&logo=readthedocs&logoColor=white)](https://millerbrainobservatory.github.io/LBM-Suite2p-Python/index.html)
+
+This package is still in a *beta* stage of development.
+
+A pipeline for processing 2-photon Light Beads Microscopy (LBM) datasets.
+
+This pipeline uses the following software:
+
+- [suite2p](https://github.com/MouseLand/suite2p)
+- [cellpose](https://github.com/MouseLand/cellpose)
+- [rastermap](https://github.com/MouseLand/rastermap)
+- [mbo_utilities](https://github.com/MillerBrainObservatory/mbo_utilities)
+- [scanreader](https://github.com/atlab/scanreader)
+
+
+[![LBM](https://zenodo.org/badge/DOI/10.1007/978-3-319-76207-4_15.svg)](https://doi.org/10.1038/s41592-021-01239-8)
+
+---
+
+## Installation
+
+See the [installation documentation](https://millerbrainobservatory.github.io/LBM-Suite2p-Python/install.html) for more details.
+
+This pipeline is fully installable with `pip`.
+
+`conda` can still be used for the virual environment, but be mindful to only install packages with `conda install` when absolutely necessary.
+
+We recommend cloning the repository, until a more established workflow is available to upload to PyPi.
+
+```
+git clone https://github.com/MillerBrainObservatory/LBM-Suite2p-Python.git
+git clone https://github.com/Suite3D # TODO
+cd LBM-Suite2p-Python
+
+# make sure your virtual environment is active
+pip install ".[all]"  # optional, contains ".[gui, notebook]"
+```
+
+---
+
+## Acknowledgements
+
+Thank you to the developers of [scanreader](https://github.com/atlab/scanreader), which provides a clean interface to ScanImage metadata using only tifffile and numpy.
+
+We vendor this repository because it is not published to an indexable Python package registry like PyPI.

lbm_suite2p_python-1.0.2/lbm_suite2p_python/VERSION

@@ -0,0 +1 @@
+1.0.2

lbm_suite2p_python-1.0.2/lbm_suite2p_python/__init__.py

@@ -0,0 +1,35 @@
+from lbm_suite2p_python.utils import *
+from lbm_suite2p_python.volume import *
+from lbm_suite2p_python.run_lsp import *
+from lbm_suite2p_python.zplane import *
+from lbm_suite2p_python.default_ops import default_ops
+
+try:
+    import suite3d
+except ImportError:
+    HAS_S3D = False
+else:
+    HAS_S3D = True
+
+__version__ = (Path(__file__).parent / "VERSION").read_text().strip()
+
+__all__ = [
+    "run_volume",
+    "run_plane",
+    "plot_traces",
+    "plot_volume_signal",
+    "plot_projection",
+    "plot_execution_time",
+    "plot_noise_distribution",
+    "animate_traces",
+    "save_images_to_movie",
+    "get_common_path",
+    "update_ops_paths",
+    "dff_percentile",
+    "dff_maxmin",
+    "dff_shot_noise",
+    "combine_tiffs",
+    "load_ops",
+    "load_planar_results",
+    "default_ops",
+]

lbm_suite2p_python-1.0.2/lbm_suite2p_python/__main__.py

@@ -0,0 +1,91 @@
+import numpy as np
+import argparse
+from pathlib import Path
+from functools import partial
+import lbm_suite2p_python as lsp
+import mbo_utilities as mbo
+
+import suite2p
+
+print = partial(print, flush=True)
+
+
+def add_args(parser: argparse.ArgumentParser):
+    """
+    Add command-line arguments to the parser, dynamically adding arguments
+    for each key in the `ops` dictionary.
+
+    Parameters
+    ----------
+    parser : argparse.ArgumentParser
+        The argument parser to which arguments are added.
+
+    Returns
+    -------
+    argparse.ArgumentParser
+        The parser with added arguments.
+    """
+
+    parser.add_argument('--version', type=str, help='Print the version of the package.')
+    parser.add_argument('--ops', type=str, help='Path to the ops .npy file.')
+    parser.add_argument('--data', type=str, help='Path to the data.')
+    parser.add_argument('--save', type=str, help='Path to save the results.')
+    parser.add_argument('--subdir', type=str, help='Additional subdirectory add to save-path.')
+    parser.add_argument('--max-depth', type=int, help='Number of subdirectories to check for files to process.')
+    parser.add_argument('--overwrite', action='store_true', help='Overwrite existing files.')
+    parser.add_argument('--skip-existing', action='store_true', help='Skip existing files.')
+
+    return parser
+
+
+def main():
+    """
+    The main function that orchestrates the CLI operations.
+    """
+    print("\n----------- LBM-Suite2p-Pipeline -----------\n")
+
+    parser = argparse.ArgumentParser(description="LBM-Suite2p-pipeline parameters")
+    parser = add_args(parser)
+    args = parser.parse_args()
+
+    if args.version:
+        print(f"lbm_suite2p_python v{lsp.__version__}")
+        return
+
+    ops = np.load(args.ops, allow_pickle=True).item() if args.ops else suite2p.default_ops()
+
+    if not args.data:
+        raise ValueError("No input file or directory specified. Use --data")
+
+    input_path = Path(args.data)
+
+    # default to data-path / 'results'
+    save_path = Path(args.save) if args.save else input_path.parent / "results"
+    save_path.mkdir(parents=True, exist_ok=True)
+
+    # Optional user-defined save folder (e.g., plane_01_runA)
+    subdir = Path(args.subdir) if args.subdir else None
+
+    if input_path.is_file():
+        output_ops = lsp.run_plane(
+            ops=ops,
+            input_tiff=input_path,
+            save_path=save_path,
+            save_folder=subdir
+        )
+    elif input_path.is_dir():
+        files = mbo.get_files(input_path, "tiff", max_depth=args.max_depth)
+        output_ops = lsp.run_volume(
+            ops=ops,
+            input_file_list=files,
+            save_path=save_path,
+            save_folder=subdir
+        )
+    else:
+        raise FileNotFoundError(f"Input path does not exist: {input_path}")
+
+    print("Processing complete -----------")
+    return output_ops
+
+if __name__ == "__main__":
+     main()

lbm_suite2p_python-1.0.2/lbm_suite2p_python/default_ops.py

@@ -0,0 +1,48 @@
+from suite2p import default_ops as s2p_default_ops
+
+def default_ops(metadata=None, ops=None, nplanes=1):
+    """
+    Returns default ops for Suite2P processing on Light Beads Microscopy datasets.
+
+    Parameters
+    ----------
+    metadata : dict, optional
+        Metadata dictionary containing information about the dataset.
+    ops : dict, str or Path, optional
+        Path to or dict of suite2p ops.
+    nplanes : int, optional
+        Number of z-planes that will be processed by Suite2p, may differ from the number of z-planes in the dataset.
+
+    Returns
+    -------
+    dict
+        Default ops for Suite2P processing.
+
+    Examples
+    --------
+    >>> import lbm_suite2p_python as lsp
+    >>> metadata = mbo.get_metadata("D://demo//raw_data//raw_file_00001.tif")  # noqa
+    >>> ops = lsp.default_ops(metadata=metadata)  # noqa
+    >>> # No ops are passed, so the default ops are used.
+    >>> lsp.run_plane(
+    >>>    ops=ops,
+    >>>    input_tiff="D://demo//raw_data//raw_file_00001.tif",
+    >>>    save_path="D://demo//results",
+    >>>    save_folder="v1"
+    >>> )
+    """
+    if ops is None:
+        ops = s2p_default_ops()
+
+    # typical neuron ~16 microns
+    ops["fs"] = metadata["frame_rate"]
+    ops["nplanes"] = 1
+    ops["nchannels"] = 1
+    ops["do_bidiphase"] = 0
+    ops["do_regmetrics"] = True
+
+    # suite2p iterates each plane and takes ops['dxy'][i] where i is the plane index
+    ops["dx"] = [metadata["pixel_resolution"][0]]
+    ops["dy"] = [metadata["pixel_resolution"][1]]
+
+    return ops