mbo_utilities 0.0.8__tar.gz

mbo_utilities-0.0.8/LICENSE.md

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+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.
+

mbo_utilities-0.0.8/PKG-INFO

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+Metadata-Version: 2.4
+Name: mbo_utilities
+Version: 0.0.8
+Summary: Various utilities for the Miller Brain Observatory
+License-Expression: BSD-3-Clause
+Project-URL: Homepage, https://github.com/millerbrainobservatory/mbo_utilities
+Project-URL: Documentation, https://millerbrainobservatory.github.io/mbo_utilities/index.html
+Project-URL: Repository, https://github.com/millerbrainobservatory/mbo_utilities
+Project-URL: Issues, https://github.com/MillerBrainObservatory/mbo_utilities/issues
+Keywords: Microscopy,ScanImage,multiROI,Tiff
+Requires-Python: <3.13,>=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: tifffile>=2025.3.30
+Requires-Dist: scikit-image
+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: ffmpeg-python
+Requires-Dist: matplotlib>=3.10.1
+Requires-Dist: h5py
+Requires-Dist: tqdm
+Provides-Extra: gui
+Requires-Dist: cmake; extra == "gui"
+Requires-Dist: imgui-bundle; extra == "gui"
+Requires-Dist: pyqt5==5.15.11; extra == "gui"
+Requires-Dist: pyqt5-qt5==5.15.2; extra == "gui"
+Requires-Dist: glfw; extra == "gui"
+Provides-Extra: notebook
+Requires-Dist: jupyter_rfb>=0.5.1; extra == "notebook"
+Requires-Dist: fastplotlib; extra == "notebook"
+Requires-Dist: pygfx; extra == "notebook"
+Requires-Dist: jupyterlab; extra == "notebook"
+Requires-Dist: sidecar; extra == "notebook"
+Requires-Dist: ipykernel; extra == "notebook"
+Requires-Dist: ipywidgets<9,>=8.0.0; extra == "notebook"
+Requires-Dist: anywidget; extra == "notebook"
+Provides-Extra: napari
+Requires-Dist: napari; extra == "napari"
+Provides-Extra: all
+Requires-Dist: imgui-bundle; extra == "all"
+Requires-Dist: pyqt5==5.15.11; extra == "all"
+Requires-Dist: pyqt5-qt5==5.15.2; extra == "all"
+Requires-Dist: glfw; extra == "all"
+Requires-Dist: jupyter_rfb>=0.5.1; extra == "all"
+Requires-Dist: fastplotlib; extra == "all"
+Requires-Dist: pygfx; extra == "all"
+Requires-Dist: jupyterlab; extra == "all"
+Requires-Dist: sidecar; extra == "all"
+Requires-Dist: ipykernel; extra == "all"
+Requires-Dist: ipywidgets<9,>=8.0.0; extra == "all"
+Requires-Dist: anywidget; extra == "all"
+Requires-Dist: napari; extra == "all"
+Dynamic: license-file
+
+# MBO utilities
+General python/shell utilities and environment/config files.
+
+## Installation
+```bash
+conda create -n mbo_util python=3.10 imgui-bundle
+conda activate mbo_util
+pip install git+https://github.com/MillerBrainObservatory/mbo_utilities.git@master
+```
+
+## Usage
+
+Open a terminal and run the following commands:
+
+``` bash
+# make sure the conda environment is activated
+mbo --path ~/data/session/
+
+# or open a dialog to select the folder
+mbo --gui
+```
+
+or in Jupyter notebook:
+
+```python
+from mbo_utilities import run_gui
+
+run_gui()
+```

mbo_utilities-0.0.8/README.md

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+# MBO utilities
+General python/shell utilities and environment/config files.
+
+## Installation
+```bash
+conda create -n mbo_util python=3.10 imgui-bundle
+conda activate mbo_util
+pip install git+https://github.com/MillerBrainObservatory/mbo_utilities.git@master
+```
+
+## Usage
+
+Open a terminal and run the following commands:
+
+``` bash
+# make sure the conda environment is activated
+mbo --path ~/data/session/
+
+# or open a dialog to select the folder
+mbo --gui
+```
+
+or in Jupyter notebook:
+
+```python
+from mbo_utilities import run_gui
+
+run_gui()
+```

mbo_utilities-0.0.8/mbo_utilities/VERSION

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+0.0.8

mbo_utilities-0.0.8/mbo_utilities/__init__.py

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+from pathlib import Path
+
+from .file_io import (
+    get_files,
+    zstack_from_files,
+    npy_to_dask,
+    read_scan,
+    save_png,
+    save_mp4,
+    zarr_to_dask,
+    expand_paths,
+)
+from .assembly import save_as
+from .metadata import is_raw_scanimage, get_metadata, params_from_metadata
+from .image import fix_scan_phase, return_scan_offset
+from .util import norm_minmax, smooth_data, is_running_jupyter
+
+from .graphics import run_gui
+
+__version__ = (Path(__file__).parent / "VERSION").read_text().strip()
+
+__all__ = [
+    "run_gui",
+    # image processing
+    "fix_scan_phase",
+    "return_scan_offset",
+    # file_io
+    "scanreader",
+    "npy_to_dask",
+    "zarr_to_dask",
+    "get_files",
+    "zstack_from_files",
+    "read_scan",
+    "save_png",
+    "save_mp4",
+    "expand_paths",
+    # metadata
+    "is_raw_scanimage",
+    "get_metadata",
+    "params_from_metadata",
+    # util
+    "norm_minmax",
+    "smooth_data",
+    "is_running_jupyter",
+    # assembly
+    "save_as",
+]

mbo_utilities-0.0.8/mbo_utilities/__main__.py

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+from __future__ import annotations
+
+import argparse
+from pathlib import Path
+
+import fastplotlib as fpl
+
+from mbo_utilities import run_gui
+
+
+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(
+        "--path",
+        type=str,
+        default=None,
+        help="Path to a directory containing raw scanimage tiff files for a single session.",
+    )
+    parser.add_argument("--gui", action="store_true", help="Run the GUI.")
+    parser.add_argument(
+        "--version", action="store_true", help="Print the version of the package."
+    )
+    return parser
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Preview a scanimage imaging session."
+        "This will display 3D [Tyx] or 4D [Tzyx] data in a GUI."
+        "The path must be a directory containing raw or assembled scanimage tiff files."
+    )
+    parser = add_args(parser)
+    args = parser.parse_args()
+
+    # Handle version
+    if args.version:
+        import mbo_utilities as mbo
+
+        print("lbm_caiman_python v{}".format(mbo.__version__))
+        return
+
+    if args.gui:
+        run_gui()
+        return
+    if not args.path or args.path == "":
+        run_gui()
+        return
+    else:
+        data_path = Path(args.path).expanduser().resolve()
+        print(f"Reading data from '{data_path}'")
+        if not data_path.exists():
+            raise FileNotFoundError(
+                f"Path '{data_path}' does not exist as a file or directory."
+            )
+        if data_path.is_dir():
+            run_gui(data_path)
+        else:
+            raise FileNotFoundError(f"Path '{data_path}' is not a directory.")
+
+
+if __name__ == "__main__":
+    main()
+    if fpl.__version__ == "0.2.0":
+        raise NotImplementedError("fastplotlib version 0.2.0 does not support GUIs.")
+    elif fpl.__version__ == "0.3.0":
+        fpl.loop.run()