peter@peter-VM:~/Documents/GitHub/Alamancy/OnkoDICOM-alamancy$ virtualenv --python=python3 venv
created virtual environment CPython3.8.10.final.0-64 in 215ms
  creator CPython3Posix(dest=/home/peter/Documents/GitHub/Alamancy/OnkoDICOM-alamancy/venv, clear=False, global=False)
  seeder FromAppData(download=False, pip=latest, setuptools=latest, wheel=latest, pkg_resources=latest, via=copy, app_data_dir=/home/peter/.local/share/virtualenv/seed-app-data/v1.0.1.debian.1)
  activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator,XonshActivator
peter@peter-VM:~/Documents/GitHub/Alamancy/OnkoDICOM-alamancy$ source venv/bin/activate
(venv) peter@peter-VM:~/Documents/GitHub/Alamancy/OnkoDICOM-alamancy$ pip install -r pre-requirements.txt 
Collecting cython
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Processing /home/peter/.cache/pip/wheels/fc/39/52/8d6f3cec1cca4ceb44d658427c35711b19d89dbc4914af657f/pandocfilters-1.4.3-py3-none-any.whl
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ERROR: rt-utils 1.1.6 has requirement pydicom==2.1.2, but you'll have pydicom 2.2.1 which is incompatible.
Installing collected packages: cython, numpy, click, dataclasses, pydicom, opencv-python, rt-utils, pytz, six, python-dateutil, pandas, SimpleITK, pynetdicom, cycler, pyparsing, kiwisolver, pillow, matplotlib, urllib3, charset-normalizer, certifi, idna, requests, ipython-genutils, tornado, debugpy, traitlets, matplotlib-inline, parso, jedi, pickleshare, backcall, pygments, ptyprocess, pexpect, wcwidth, prompt-toolkit, decorator, ipython, jupyter-core, nest-asyncio, pyzmq, entrypoints, jupyter-client, ipykernel, pyrsistent, attrs, jsonschema, nbformat, nbclient, packaging, webencodings, bleach, mistune, jupyterlab-pygments, pandocfilters, MarkupSafe, jinja2, testpath, defusedxml, nbconvert, Send2Trash, pycparser, cffi, argon2-cffi, terminado, prometheus-client, notebook, widgetsnbextension, jupyterlab-widgets, ipywidgets, tifffile, PyWavelets, networkx, imageio, scipy, scikit-image, loguru, typing-extensions, pymedphys, hyperlink, cryptography, txaio, autobahn, zope.interface, incremental, constantly, Automat, Twisted, async-timeout, multidict, chardet, yarl, aiohttp, wslink, vtk, seaborn, platipy
Successfully installed Automat-20.2.0 MarkupSafe-2.0.1 PyWavelets-1.1.1 Send2Trash-1.8.0 SimpleITK-2.1.1 Twisted-21.7.0 aiohttp-3.7.4.post0 argon2-cffi-21.1.0 async-timeout-3.0.1 attrs-21.2.0 autobahn-21.3.1 backcall-0.2.0 bleach-4.1.0 certifi-2021.5.30 cffi-1.14.6 chardet-4.0.0 charset-normalizer-2.0.4 click-8.0.1 constantly-15.1.0 cryptography-3.4.8 cycler-0.10.0 cython-0.29.24 dataclasses-0.6 debugpy-1.4.3 decorator-5.1.0 defusedxml-0.7.1 entrypoints-0.3 hyperlink-21.0.0 idna-3.2 imageio-2.9.0 incremental-21.3.0 ipykernel-6.4.1 ipython-7.27.0 ipython-genutils-0.2.0 ipywidgets-7.6.4 jedi-0.18.0 jinja2-3.0.1 jsonschema-3.2.0 jupyter-client-7.0.2 jupyter-core-4.7.1 jupyterlab-pygments-0.1.2 jupyterlab-widgets-1.0.1 kiwisolver-1.3.2 loguru-0.5.3 matplotlib-3.3.4 matplotlib-inline-0.1.3 mistune-0.8.4 multidict-5.1.0 nbclient-0.5.4 nbconvert-6.1.0 nbformat-5.1.3 nest-asyncio-1.5.1 networkx-2.6.3 notebook-6.4.3 numpy-1.21.0 opencv-python-4.5.3.56 packaging-21.0 pandas-1.3.2 pandocfilters-1.4.3 parso-0.8.2 pexpect-4.8.0 pickleshare-0.7.5 pillow-8.3.2 platipy-0.1.2 prometheus-client-0.11.0 prompt-toolkit-3.0.20 ptyprocess-0.7.0 pycparser-2.20 pydicom-2.2.1 pygments-2.10.0 pymedphys-0.37.1 pynetdicom-1.5.7 pyparsing-2.4.7 pyrsistent-0.18.0 python-dateutil-2.8.2 pytz-2021.1 pyzmq-22.2.1 requests-2.26.0 rt-utils-1.1.6 scikit-image-0.17.2 scipy-1.7.1 seaborn-0.11.2 six-1.16.0 terminado-0.12.1 testpath-0.5.0 tifffile-2021.8.30 tornado-6.1 traitlets-5.1.0 txaio-21.2.1 typing-extensions-3.10.0.2 urllib3-1.26.6 vtk-9.0.3 wcwidth-0.2.5 webencodings-0.5.1 widgetsnbextension-3.5.1 wslink-1.0.7 yarl-1.6.3 zope.interface-5.4.0
(venv) peter@peter-VM:~/Documents/GitHub/Alamancy/OnkoDICOM-alamancy$ python main.py
Traceback (most recent call last):
  File "main.py", line 6, in <module>
    from PySide6 import QtWidgets, QtCore
ModuleNotFoundError: No module named 'PySide6'
(venv) peter@peter-VM:~/Documents/GitHub/Alamancy/OnkoDICOM-alamancy$ pip install -r requirements.txt 
Ignoring dataclasses: markers 'python_version == "3.6.*"' don't match your environment
Collecting git+https://github.com/Radiomics/pyradiomics.git (from -r requirements.txt (line 14))
  Cloning https://github.com/Radiomics/pyradiomics.git to /tmp/pip-req-build-kqheo8un
  Running command git clone -q https://github.com/Radiomics/pyradiomics.git /tmp/pip-req-build-kqheo8un
Collecting git+https://github.com/matplotlib/matplotlib.git (from -r requirements.txt (line 19))
  Cloning https://github.com/matplotlib/matplotlib.git to /tmp/pip-req-build-s7hjru5i
  Running command git clone -q https://github.com/matplotlib/matplotlib.git /tmp/pip-req-build-s7hjru5i
Collecting alphashape
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Requirement already satisfied: pandas in ./venv/lib/python3.8/site-packages (from -r requirements.txt (line 2)) (1.3.2)
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Requirement already satisfied: pydicom in ./venv/lib/python3.8/site-packages (from -r requirements.txt (line 6)) (2.2.1)
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Requirement already satisfied: scikit-image in ./venv/lib/python3.8/site-packages (from -r requirements.txt (line 8)) (0.17.2)
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Requirement already satisfied: PyWavelets==1.1.1 in ./venv/lib/python3.8/site-packages (from -r requirements.txt (line 10)) (1.1.1)
Requirement already satisfied: networkx in ./venv/lib/python3.8/site-packages (from -r requirements.txt (line 12)) (2.6.3)
Requirement already satisfied: pymedphys<=0.37.1,>=0.35 in ./venv/lib/python3.8/site-packages (from -r requirements.txt (line 13)) (0.37.1)
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Requirement already satisfied: vtk in ./venv/lib/python3.8/site-packages (from -r requirements.txt (line 18)) (9.0.3)
Requirement already satisfied: SimpleITK>=0.9.1 in ./venv/lib/python3.8/site-packages (from pyradiomics==3.0.1.post4+gad5b2de->-r requirements.txt (line 14)) (2.1.1)
Requirement already satisfied: numpy>=1.9.2 in ./venv/lib/python3.8/site-packages (from pyradiomics==3.0.1.post4+gad5b2de->-r requirements.txt (line 14)) (1.21.0)
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Requirement already satisfied: six>=1.10.0 in ./venv/lib/python3.8/site-packages (from pyradiomics==3.0.1.post4+gad5b2de->-r requirements.txt (line 14)) (1.16.0)
Requirement already satisfied: cycler>=0.10 in ./venv/lib/python3.8/site-packages (from matplotlib==3.5.0.dev1928+g0666c59edb->-r requirements.txt (line 19)) (0.10.0)
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Requirement already satisfied: kiwisolver>=1.0.1 in ./venv/lib/python3.8/site-packages (from matplotlib==3.5.0.dev1928+g0666c59edb->-r requirements.txt (line 19)) (1.3.2)
Requirement already satisfied: packaging>=20.0 in ./venv/lib/python3.8/site-packages (from matplotlib==3.5.0.dev1928+g0666c59edb->-r requirements.txt (line 19)) (21.0)
Requirement already satisfied: pillow>=6.2.0 in ./venv/lib/python3.8/site-packages (from matplotlib==3.5.0.dev1928+g0666c59edb->-r requirements.txt (line 19)) (8.3.2)
Requirement already satisfied: pyparsing>=2.2.1 in ./venv/lib/python3.8/site-packages (from matplotlib==3.5.0.dev1928+g0666c59edb->-r requirements.txt (line 19)) (2.4.7)
Requirement already satisfied: python-dateutil>=2.7 in ./venv/lib/python3.8/site-packages (from matplotlib==3.5.0.dev1928+g0666c59edb->-r requirements.txt (line 19)) (2.8.2)
Collecting setuptools_scm>=4
  Using cached setuptools_scm-6.3.1-py3-none-any.whl (33 kB)
Collecting trimesh>=3.9.8
  Using cached trimesh-3.9.29-py3-none-any.whl (635 kB)
Collecting shapely>=1.4.0
  Using cached Shapely-1.7.1-cp38-cp38-manylinux1_x86_64.whl (1.0 MB)
Collecting rtree>=0.9.7
  Using cached Rtree-0.9.7-cp38-cp38-manylinux2010_x86_64.whl (994 kB)
Collecting click-log>=0.3.2
  Using cached click_log-0.3.2-py2.py3-none-any.whl (4.6 kB)
Requirement already satisfied: Click>=6.0 in ./venv/lib/python3.8/site-packages (from alphashape->-r requirements.txt (line 1)) (8.0.1)
Requirement already satisfied: pytz>=2017.3 in ./venv/lib/python3.8/site-packages (from pandas->-r requirements.txt (line 2)) (2021.1)
Collecting distro
  Using cached distro-1.6.0-py2.py3-none-any.whl (19 kB)
Requirement already satisfied: wheel>=0.29.0 in ./venv/lib/python3.8/site-packages (from scikit-build->-r requirements.txt (line 3)) (0.34.2)
Requirement already satisfied: setuptools>=28.0.0; python_version >= "3" in ./venv/lib/python3.8/site-packages (from scikit-build->-r requirements.txt (line 3)) (44.0.0)
Requirement already satisfied: imageio>=2.3.0 in ./venv/lib/python3.8/site-packages (from scikit-image->-r requirements.txt (line 8)) (2.9.0)
Requirement already satisfied: tifffile>=2019.7.26 in ./venv/lib/python3.8/site-packages (from scikit-image->-r requirements.txt (line 8)) (2021.8.30)
Requirement already satisfied: typing-extensions in ./venv/lib/python3.8/site-packages (from pymedphys<=0.37.1,>=0.35->-r requirements.txt (line 13)) (3.10.0.2)
Requirement already satisfied: attrs>=19.2.0 in ./venv/lib/python3.8/site-packages (from pytest->-r requirements.txt (line 16)) (21.2.0)
Collecting toml
  Using cached toml-0.10.2-py2.py3-none-any.whl (16 kB)
Collecting pluggy<2.0,>=0.12
  Using cached pluggy-1.0.0-py2.py3-none-any.whl (13 kB)
Collecting py>=1.8.2
  Using cached py-1.10.0-py2.py3-none-any.whl (97 kB)
Collecting iniconfig
  Using cached iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB)
Collecting shiboken6==6.1.2
  Using cached shiboken6-6.1.2-6.1.2-cp36.cp37.cp38.cp39-abi3-manylinux1_x86_64.whl (1.1 MB)
Requirement already satisfied: Twisted>=17.5.0 in ./venv/lib/python3.8/site-packages (from vtk->-r requirements.txt (line 18)) (21.7.0)
Requirement already satisfied: wslink>=0.1.3 in ./venv/lib/python3.8/site-packages (from vtk->-r requirements.txt (line 18)) (1.0.7)
Requirement already satisfied: autobahn>=17.7.1 in ./venv/lib/python3.8/site-packages (from vtk->-r requirements.txt (line 18)) (21.3.1)
Collecting ruamel.yaml>=0.16.0
  Using cached ruamel.yaml-0.17.16-py3-none-any.whl (109 kB)
Processing /home/peter/.cache/pip/wheels/56/ea/58/ead137b087d9e326852a851351d1debf4ada529b6ac0ec4e8c/docopt-0.6.2-py2.py3-none-any.whl
Collecting tomli>=1.0.0
  Using cached tomli-1.2.1-py3-none-any.whl (11 kB)
Requirement already satisfied: zope.interface>=4.4.2 in ./venv/lib/python3.8/site-packages (from Twisted>=17.5.0->vtk->-r requirements.txt (line 18)) (5.4.0)
Requirement already satisfied: incremental>=21.3.0 in ./venv/lib/python3.8/site-packages (from Twisted>=17.5.0->vtk->-r requirements.txt (line 18)) (21.3.0)
Requirement already satisfied: hyperlink>=17.1.1 in ./venv/lib/python3.8/site-packages (from Twisted>=17.5.0->vtk->-r requirements.txt (line 18)) (21.0.0)
Requirement already satisfied: constantly>=15.1 in ./venv/lib/python3.8/site-packages (from Twisted>=17.5.0->vtk->-r requirements.txt (line 18)) (15.1.0)
Requirement already satisfied: Automat>=0.8.0 in ./venv/lib/python3.8/site-packages (from Twisted>=17.5.0->vtk->-r requirements.txt (line 18)) (20.2.0)
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Requirement already satisfied: txaio>=21.2.1 in ./venv/lib/python3.8/site-packages (from autobahn>=17.7.1->vtk->-r requirements.txt (line 18)) (21.2.1)
Requirement already satisfied: cryptography>=3.4.6 in ./venv/lib/python3.8/site-packages (from autobahn>=17.7.1->vtk->-r requirements.txt (line 18)) (3.4.8)
Collecting ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.10"
  Using cached ruamel.yaml.clib-0.2.6-cp38-cp38-manylinux1_x86_64.whl (570 kB)
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Requirement already satisfied: yarl<2.0,>=1.0 in ./venv/lib/python3.8/site-packages (from aiohttp->wslink>=0.1.3->vtk->-r requirements.txt (line 18)) (1.6.3)
Requirement already satisfied: chardet<5.0,>=2.0 in ./venv/lib/python3.8/site-packages (from aiohttp->wslink>=0.1.3->vtk->-r requirements.txt (line 18)) (4.0.0)
Requirement already satisfied: multidict<7.0,>=4.5 in ./venv/lib/python3.8/site-packages (from aiohttp->wslink>=0.1.3->vtk->-r requirements.txt (line 18)) (5.1.0)
Requirement already satisfied: async-timeout<4.0,>=3.0 in ./venv/lib/python3.8/site-packages (from aiohttp->wslink>=0.1.3->vtk->-r requirements.txt (line 18)) (3.0.1)
Requirement already satisfied: cffi>=1.12 in ./venv/lib/python3.8/site-packages (from cryptography>=3.4.6->autobahn>=17.7.1->vtk->-r requirements.txt (line 18)) (1.14.6)
Requirement already satisfied: pycparser in ./venv/lib/python3.8/site-packages (from cffi>=1.12->cryptography>=3.4.6->autobahn>=17.7.1->vtk->-r requirements.txt (line 18)) (2.20)
Building wheels for collected packages: pyradiomics, matplotlib
  Building wheel for pyradiomics (setup.py) ... done
  Created wheel for pyradiomics: filename=pyradiomics-3.0.1.post4+gad5b2de-cp38-cp38-linux_x86_64.whl size=190874 sha256=c55037d2899a9bca169c81ed5ad89c8935d81ca10fb73b35e70309926c1b9056
  Stored in directory: /tmp/pip-ephem-wheel-cache-xvcsb2ud/wheels/cb/9c/ee/aab64bab2f0555c2b911887825a802ece83a12e1017bf47320
  Building wheel for matplotlib (setup.py) ... done
  Created wheel for matplotlib: filename=matplotlib-3.5.0.dev1928+g0666c59edb-cp38-cp38-linux_x86_64.whl size=10538444 sha256=ce95221aca237aeba88a4427e69b8eca279d444aac2c93b915378e63f7b5b8a1
  Stored in directory: /tmp/pip-ephem-wheel-cache-xvcsb2ud/wheels/d6/12/df/a85dab096823c7538f324ac187bd39afaa72ee447fbeabf5ba
Successfully built pyradiomics matplotlib
ERROR: platipy 0.1.2 has requirement matplotlib<3.4.0,>=3.3.4, but you'll have matplotlib 3.5.0.dev1928+g0666c59edb which is incompatible.
Installing collected packages: trimesh, shapely, rtree, click-log, alphashape, distro, scikit-build, fonttools, tomli, setuptools-scm, matplotlib, dicompyler-core, country-list, fuzzywuzzy, toml, pluggy, py, iniconfig, pytest, pytest-qt, shiboken6, pyside6, ruamel.yaml.clib, ruamel.yaml, docopt, pykwalify, pyradiomics
  Attempting uninstall: matplotlib
    Found existing installation: matplotlib 3.3.4
    Uninstalling matplotlib-3.3.4:
      Successfully uninstalled matplotlib-3.3.4
Successfully installed alphashape-1.3.1 click-log-0.3.2 country-list-1.0.0 dicompyler-core-0.5.5 distro-1.6.0 docopt-0.6.2 fonttools-4.26.2 fuzzywuzzy-0.18.0 iniconfig-1.1.1 matplotlib-3.5.0.dev1928+g0666c59edb pluggy-1.0.0 py-1.10.0 pykwalify-1.8.0 pyradiomics-3.0.1.post4+gad5b2de pyside6-6.1.2 pytest-6.2.5 pytest-qt-4.0.2 rtree-0.9.7 ruamel.yaml-0.17.16 ruamel.yaml.clib-0.2.6 scikit-build-0.12.0 setuptools-scm-6.3.1 shapely-1.7.1 shiboken6-6.1.2 toml-0.10.2 tomli-1.2.1 trimesh-3.9.29
(venv) peter@peter-VM:~/Documents/GitHub/Alamancy/OnkoDICOM-alamancy$ python main.py
/home/peter/Documents/GitHub/Alamancy/OnkoDICOM-alamancy/venv/lib/python3.8/site-packages/fuzzywuzzy/fuzz.py:11: UserWarning: Using slow pure-python SequenceMatcher. Install python-Levenshtein to remove this warning
  warnings.warn('Using slow pure-python SequenceMatcher. Install python-Levenshtein to remove this warning')
PDPI: 95.91369331501092

