FlowMePy - a Python API for FlowMe

Load FCS 2.0/3.0/3.1 files with super fast C++ code. The FCS processing includes compensation and logicle transform. If FacsDiva projects (XMLs) or Kaluza projects (analysis) are provided, the FlowMePy will label events according to the gates contained.

Read the Docs

Install

We provide a pre-compiled package (currently Windows only) which can be installed using:

pip install flowmepy

Dependencies

• python (>= 3.6)
• CMake (>= 3.14.1)
• Qt SDK or the compiled sources (>= 5.11.0)
• OpenCV (>= 4.0.0)
• Visual Studio (>= 2015) or gcc

Configure FlowMe using CMake (Windows only)

• dir to ./flowme
• copy CMakeUserPathsGit.cmake and rename it to CMakeUserPaths.cmake
• add your library paths to the ${CMAKE_PREFIX_PATH} in CMakeUserPaths.cmake

Clone

We use submodules for flowme and pybind11 if you clone using

$ git clone --recursive git@smithers.cvl.tuwien.ac.at:kwc/dev/flowme-python-api.git

everything should be fine. In case the repository's flowme or pybind11 folders are empty, check if the pull worked as expected:

• don't forget --recursive
• windows users: it's easiest if you do not password protect the ssh key

Build

$ virtualenv env
$ source /env/bin/activate
$ python setup.py install

If anything did not work as expected, try building FlowMe as standalone package (see README). Then run the above command again.

You can remove old versions using pip:

$ pip uninstall FlowMePy
Successfully uninstalled flowmepy-0.0.3

Packaging FlowMePy

Update pip (on Windows & Linux), then create the wheel:

python -m pip install --upgrade setuptools wheel
python setup.py sdist bdist_wheel

where sdist creates the source archive (without C++ files) and bdist_wheel creates the build package.

Then, upload the package:

python -m twine upload dist/*

in case you want to test your package, use this for uploading:

python -m twine upload --repository-url https://test.pypi.org/legacy/ dist/*

Unfortunately, test.pypi.org rejects linux binary wheels - so linux users must build packages on their own. You can install this package using:

pip install -i https://test.pypi.org/simple/ flowmepy --extra-index-url https://pypi.org/simple

Test

Test flowmepy using:

$ python -m unittest discover -v test

build the docs

$ cd docs
$ make html

The compiled docs are here: docs/_build/index.html

FlowMePy in 2 minutes

load an FCS using

import flowme

filepath = "./flowme/src/data/samples/FacsDiva.xml"
sample = flowme.fcs(filepath)
events = sample.events()       # get the event data (pandas.DataFrame)
gates = sample.gate_labels()   # get gating (GT) information (pandas.DataFrame)

Per default events are not filtered by any Gate. However, it is possible to pass the name of a filtering gate:

import flowme

filepath = "./flowme/src/data/samples/FacsDiva.xml"
filter_gatename = "viable"
sample = flowme.fcs(filepath, filter_gatename)

FlowMe provides a built-in data cleaning function that prunes events accumulated at the measured maximum.

import flowme

filepath = "./flowme/src/data/samples/FacsDiva.xml"
sample = flowme.fcs(filepath)
events, gates = sample.filtered_data(cleanDataPercent=0.001)

Handling multi tube files

Some files may contain multiple tubes. The following code shows how available tubes can be queried as well as how to select from which tube to load the data.

import flowme


tube_names = sample.get_tube_names()
sample.set_tube_index(len(tub_names) - 1)
events = sample.events() #events of last tube in sample