About

Slitflow is developed in https://github.com/yumaitou/slitflow/.
The documentation can be found at https://slitflow.readthedocs.io.
Slitflow can be installed from https://pypi.org/project/slitflow/.

Citation

If Slitflow was useful for your research, please consider citing the following our paper:

Ito, Y., Hirose, M., and Tokunaga, M. (2023). Slitflow: A Python framework for single-molecule dynamics and localization analysis. SoftwareX 23, 101462. 10.1016/j.softx.2023.101462.

Environments

Slitflow is tested on the following operating systems.

Windows10
Windows11
macOS Ventura 13
Ubuntu 22.04.1

Dependencies

The basic slitflow has the following dependencies:

numpy
pandas
matplotlib
tifffile
tqdm
psutil
opencv-python
scipy
scikit-learn
scikit-image

License

Slitflow is distributed under the BSD 3-Clause License.

BSD 3-Clause License

Copyright (c) 2022-2023, Yuma Ito and contributors

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.

Changelog

Slitflow follows major version zero (rapid development) of Semantic Versioning.

0.1.5 (2023-11-01)

Internal Changes

Updated the internal functions for index operations related to file splitting. Note that the input/output and behavior of the Data and Pipeline classes remain unchanged, allowing users to utilize the update seamlessly without any awareness of the changes made.

0.1.4 (2023-10-30)

Features

Added slitflow.trj.subtrj.Subtrajectory class.
Added the type parameter to slitflow.img.noise.Gauss class.

API changes

Updated slitflow.tbl.convert.SortCols to be able to sort all columns, resulting in a change in the process parameters.

Documentation

Updated the citation.
Improved API documentation.
Added pdf and epub documentation.

Bug fixes

Deleted the incorrect default argument of slitflow.name.load_data_paths().
Changed the colabo badge link to the local PNG image.
Fixed minor bugs.

0.1.3 (2023-06-02)

API changes

Renamed slitflow.info.Info.to_string() to slitflow.info.Info.to_json().

0.1.2 (2023-05-19)

Features

Updated getting started for Gitpod and Colab.
Updated requirements.
Added slitflow.tbl.proc.SelectParam class.
Added slitflow.img.proc.SelectParam class.
Added slitflow.img.create.CheckerBoard class.

API changes

Changed slitflow.img.create.Black class parameters.

Bug fixes

Fixed bug related to slitflow.img.proc.SelectParam class. See “Add SelectParam and fix related bugs” commit.
Fixed bug in ModelJumpLenDist creating table indices inappropriately.

0.1.1 (2023-03-07)

Features

Updated the documentation.
Added slitflow.img.noise.Gauss class.
Added tests using pytest.
Added example scripts.

API changes

Changed to Python <3.11 due to dependency on scikit-image.

Bug fixes

Fixed bug in ToTiff raising ValueError related to matplotlib.Figure.canvas.draw on macOS backend.
Fixed bug in set_grp_name related to loading CSV files.
Fixed bug related to splitting depth in figure classes.
Fixed bug in Image splitting data inappropriately.

Identified issues

Bug in the drawing figure, probably caused by matplotlib figure refresh.
slitflow.img.plot.Gauss2D requires specific split depth of reqs data.

0.1.0 (2023-02-02)

Features

Added basic functionality.

0.0.1 (2022-10-29)

Features

Added test code.