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PyECVL is a Python wrapper for ECVL, the European Computer Vision Library.

Each PyECVL version requires a specific ECVL version:

PyECVL version	ECVL version
0.1.0	0.1.0

Quick start

The following assumes you have ECVL already installed in "standard" system paths (e.g., /usr/local/include, /usr/local/lib).

git clone --recurse-submodules https://github.com/deephealthproject/pyecvl.git
cd pyecvl
python3 -m pip install numpy pybind11 pytest
python3 setup.py install

See full installation instructions below.

Getting started

import numpy as np
import pyecvl._core.ecvl as ecvl

def inc_brightness(img, rate):
    a = np.array(img, copy=False)
    max_val = np.iinfo(a.dtype).max
    a[a > max_val - rate] = max_val
    a[a <= max_val - rate] += rate

def main():
    img = ecvl.ImRead("test.jpg")
    inc_brightness(img, 10)
    ecvl.ImWrite("test_mod.jpg", img)

if __name__ == "__main__":
    main()

Installation

Requirements

• Python 3
• ECVL
• NumPy
• pybind11
• pytest (if you want to run the tests)

ECVL Installation

Complete ECVL installation instructions are available at https://github.com/deephealthproject/ecvl. Here is a sample build sequence:

git clone --recurse-submodules https://github.com/deephealthproject/pyecvl.git
cd third_party/ecvl
mkdir build
cd build
cmake -DECVL_WITH_DICOM=ON -DECVL_WITH_OPENSLIDE=ON -DECVL_DATASET_PARSER=ON -DECVL_BUILD_EDDL=ON ..
make
make install

PyECVL installation

Install PyECVL as follows:

python3 -m pip install numpy pybind11 pytest
python3 setup.py install

Then, you can test your installation by running the PyECVL tests:

pytest tests

Disabling unwanted modules

By default, PyECVL assumes a complete ECVL installation, including optional modules (except for the GUI), and builds bindings for all of them. You can disable support for specific modules via environment variables. For instance, suppose you installed ECVL without openslide support: by default, PyECVL will try to build the bindings for openslide-specific ECVL tools and link the openslide library, which might not even be present on your system. To avoid this, set the ECVL_WITH_OPENSLIDE environment variable to OFF (or FALSE) before building PyECVL. Similarly, you can turn off DICOM and EDDL support by setting ECVL_WITH_DICOM and ECVL_EDDL to OFF.

ECVL installed in an arbitrary directory

The above installation instructions assume ECVL has been installed in standard system paths. However, ECVL can be installed in an arbitrary directory, for instance:

cd third_party/ecvl
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=/home/myuser/ecvl -DECVL_WITH_DICOM=ON -DECVL_WITH_OPENSLIDE=ON -DECVL_DATASET_PARSER=ON -DECVL_BUILD_EDDL=ON ..
make
make install

You can tell the PyECVL setup script about this via the ECVL_DIR environment variable:

export ECVL_DIR=/home/myuser/ecvl
python3 setup.py install

In this way, setup.py will look for additional include files in /home/myuser/ecvl/include and for additional libraries in /home/myuser/ecvl/lib.

Similarly, if EDDL is installed in an arbitrary path, you can tell the setup script via the EDDL_DIR environment variable.