notmatthancock

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
A script to get the version of Python by which the file was compiled
"""

from __future__ import print_function

import binascii
import os

notmatthancock

# Run flake8 only on new files according to git-diff
# 
# If run with no arguments, i.e.,
#     $ dflake8
# then the diff is taken against the master branch.
# If run with a single argument, then that argument is used for diff'ing, i.e.,
#     $ dflake8 feature-branch
# or
#     $ dflake8 HEAD
dflake8 () {

notmatthancock

import matplotlib.pyplot as plt
import numpy as np
from sklearn import datasets as ds
from sklearn.ensemble import RandomForestRegressor
from sklearn.model_selection import cross_val_score


# Number of folds to use for CV
N_FOLDS = 5

notmatthancock

import pylidc as pl
import numpy as np
import matplotlib.pyplot as plt
from skimage.viewer import CollectionViewer

# Load scan, convert to volume.
scan = pl.query(pl.Scan).filter(pl.Scan.patient_id == "LIDC-IDRI-0001").first()
vol = scan.to_volume(verbose=False)

# mask_vol is a boolean, indicator volume for the first annotation of the scan.

notmatthancock

sudo apt-get remove mayavi2
sudo apt-get autoremove
sudo apt-get install libvtk5.10-qt4 # I use leave off qt4. I use qt backend.
sudo apt-get install python-vtk
sudo apt-get install python-traits
sudo apt-get install libvtk5-dev
sudo pip install sphinx

cd ~/Downloads # or whatever temporary dir.
wget https://github.com/enthought/mayavi/archive/4.5.0.zip

notmatthancock

# cython windowize.pyx
# gcc -shared -pthread -fPIC -fwrapv -O2 -Wall -fno-strict-aliasing -I/usr/include/python2.7 -o windowize.so windowize.c

import numpy as np
cimport numpy as np
cimport cython

DTYPE = np.float64
ctypedef np.float64_t dtype_t

notmatthancock

import sys
import numpy as np
import matplotlib.pyplot as plt
import theano
import theano.tensor as T

rs = np.random.RandomState(1234)

def gen_spiral(label, dt, n_samples=100, noise=0.1):
    """

notmatthancock

^CTraceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib-1.4.x-py2.7-macosx-10.6-x86_64.egg/matplotlib/pyplot.py", line 27, in <module>
    import matplotlib.colorbar
  File "/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib-1.4.x-py2.7-macosx-10.6-x86_64.egg/matplotlib/colorbar.py", line 34, in <module>
    import matplotlib.collections as collections
  File "/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib-1.4.x-py2.7-macosx-10.6-x86_64.egg/matplotlib/collections.py", line 27, in <module>
    import matplotlib.backend_bases as backend_bases
  File "/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib-1.4.x-py2.7-macosx-10.6-x86_64.egg/matplotlib/backend_bases.py", line 56, in <module>
    impor