ASAP installation and usage

I did this under python3.5, which is the default version for python3 in Ubuntu

sudo apt-get install python3-tk
sudo apt-get install libpython3.6-dev
pip3 install matplotlib numpy


then download ASAP from the website: https://github.com/computationalpathologygroup/ASAP/releases

and install it by the command:
dpkg -i ASAP-1.8-python36-Linux.deb

to find where it was installed, use the command:

dpkg -L asap

Now, we put it in the PYTHONPATH:

PYTHONPATH="/opt/ASAP/bin":"${PYTHONPATH}"
 export PYTHONPATH


now we can begin

type command : python3

then we enter python,



>>>import matplotlib.pyplot as plt
>>> import multiresolutionimageinterface as mir
>>> reader = mir.MultiResolutionImageReader()
>>>mr_image = reader.open('/home/wli/Downloads/tumor_036.tif')

>>>tile = mr_image.getUCharPatch(0, 0, dims[0], dims[1], 6)

>>> plt.imshow(tile)

>>> plt.show()

>>> tile =mr_image.getUCharPatch(37000, 90000, 1024, 1024, 0)
>>> plt.imshow(tile)
>>>plt.show()

or using openslide
slide = openslide.open_slide(slide_path)

thumbnail = slide.get_thumbnail((slide.dimensions[0] / 256, slide.dimensions[1] / 256))