sip-aau/magni

A package for AFM image reconstruction and compressed sensing in general

magni's Issues

The utils-multiprocessing.ipynb example does not work on Mac OS X without MKL

This bug is not caused by magni but rather numpy (or multiprocessing). It is present on Mac OS X for versions of Python and numpy that have not been compiled against MKL. The following piece of code illustrates the problem:

import multiprocessing as mp

import numpy as np


def compute(n):
    print('Enter')
    np.dot(np.eye(n), np.eye(n))
    print('Exit')


print('\nWithout multiprocessing:')
compute(1000)

print('\nWith multiprocessing:')
workers = mp.Pool(1)
results = workers.map(compute, (1000, 1000))

The above code hangs in the workers.map call when executing np.dot(np.eye(n), np.eye(n)). Strangely, there is no problem if the non-multiprocessing call to compute is ommitted, or the value of n is reduced sufficiently.

“not defined” errors in the doctests

I'm seeing a number of “not defined” errors in the doctests, in both Python 3.3 and 2.7, when run with nosetests:

$ nosetests --with-doctest --doctest-tests magni
FFFFF..FFF....F...........F...FFF..FF...F..
======================================================================
FAIL: Doctest: magni.afm.io.read_mi_file
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib64/python3.3/doctest.py", line 2179, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for magni.afm.io.read_mi_file
  File "/.../magni/afm/io.py", line 46, in read_mi_file

----------------------------------------------------------------------
File "/.../magni/afm/io.py", line 73, in magni.afm.io.read_mi_file
Failed example:
    path = magni.utils.split_path(magni.__path__[0])[0]
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.io.read_mi_file[1]>", line 1, in <module>
        path = magni.utils.split_path(magni.__path__[0])[0]
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/io.py", line 74, in magni.afm.io.read_mi_file
Failed example:
    path = path + 'examples' + os.sep + 'example.mi'
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.io.read_mi_file[2]>", line 1, in <module>
        path = path + 'examples' + os.sep + 'example.mi'
    NameError: name 'path' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/io.py", line 75, in magni.afm.io.read_mi_file
Failed example:
    mi_file = read_mi_file(path)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.io.read_mi_file[3]>", line 1, in <module>
        mi_file = read_mi_file(path)
    NameError: name 'path' is not defined


======================================================================
FAIL: Doctest: magni.afm.reconstruction.analyse
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib64/python3.3/doctest.py", line 2179, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for magni.afm.reconstruction.analyse
  File "/.../magni/afm/reconstruction.py", line 63, in analyse

----------------------------------------------------------------------
File "/.../magni/afm/reconstruction.py", line 93, in magni.afm.reconstruction.analyse
Failed example:
    path = magni.utils.split_path(magni.__path__[0])[0]
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.reconstruction.analyse[1]>", line 1, in <module>
        path = magni.utils.split_path(magni.__path__[0])[0]
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/reconstruction.py", line 94, in magni.afm.reconstruction.analyse
Failed example:
    path = path + 'examples' + os.sep + 'example.mi'
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.reconstruction.analyse[2]>", line 1, in <module>
        path = path + 'examples' + os.sep + 'example.mi'
    NameError: name 'path' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/reconstruction.py", line 95, in magni.afm.reconstruction.analyse
Failed example:
    mi_file = magni.afm.io.read_mi_file(path)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.reconstruction.analyse[3]>", line 1, in <module>
        mi_file = magni.afm.io.read_mi_file(path)
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/reconstruction.py", line 96, in magni.afm.reconstruction.analyse
Failed example:
    mi_buffer = mi_file.get_buffer('Topography')[0]
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.reconstruction.analyse[4]>", line 1, in <module>
        mi_buffer = mi_file.get_buffer('Topography')[0]
    NameError: name 'mi_file' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/reconstruction.py", line 97, in magni.afm.reconstruction.analyse
Failed example:
    mi_data = mi_buffer.get_data()
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.reconstruction.analyse[5]>", line 1, in <module>
        mi_data = mi_buffer.get_data()
    NameError: name 'mi_buffer' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/reconstruction.py", line 98, in magni.afm.reconstruction.analyse
Failed example:
    x = magni.imaging.mat2vec(mi_data)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.reconstruction.analyse[6]>", line 1, in <module>
        x = magni.imaging.mat2vec(mi_data)
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/reconstruction.py", line 111, in magni.afm.reconstruction.analyse
Failed example:
    Phi = magni.utils.matrices.Matrix(Phi_A, Phi_T, (),
                                      (int(len(x) / 2), len(x)))
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.reconstruction.analyse[9]>", line 1, in <module>
        Phi = magni.utils.matrices.Matrix(Phi_A, Phi_T, (),
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/reconstruction.py", line 117, in magni.afm.reconstruction.analyse
Failed example:
    Psi = magni.imaging.dictionaries.get_DCT(mi_data.shape)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.reconstruction.analyse[10]>", line 1, in <module>
        Psi = magni.imaging.dictionaries.get_DCT(mi_data.shape)
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/reconstruction.py", line 121, in magni.afm.reconstruction.analyse
Failed example:
    print('MSE: {:.2f}, PSNR: {:.2f}'.format(*analyse(x, Phi, Psi)))
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.reconstruction.analyse[11]>", line 1, in <module>
        print('MSE: {:.2f}, PSNR: {:.2f}'.format(*analyse(x, Phi, Psi)))
    NameError: name 'x' is not defined


======================================================================
FAIL: Doctest: magni.afm.reconstruction.reconstruct
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib64/python3.3/doctest.py", line 2179, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for magni.afm.reconstruction.reconstruct
  File "/.../magni/afm/reconstruction.py", line 168, in reconstruct

----------------------------------------------------------------------
File "/.../magni/afm/reconstruction.py", line 198, in magni.afm.reconstruction.reconstruct
Failed example:
    path = magni.utils.split_path(magni.__path__[0])[0]
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.reconstruction.reconstruct[1]>", line 1, in <module>
        path = magni.utils.split_path(magni.__path__[0])[0]
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/reconstruction.py", line 199, in magni.afm.reconstruction.reconstruct
Failed example:
    path = path + 'examples' + os.sep + 'example.mi'
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.reconstruction.reconstruct[2]>", line 1, in <module>
        path = path + 'examples' + os.sep + 'example.mi'
    NameError: name 'path' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/reconstruction.py", line 200, in magni.afm.reconstruction.reconstruct
Failed example:
    mi_file = magni.afm.io.read_mi_file(path)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.reconstruction.reconstruct[3]>", line 1, in <module>
        mi_file = magni.afm.io.read_mi_file(path)
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/reconstruction.py", line 201, in magni.afm.reconstruction.reconstruct
Failed example:
    mi_buffer = mi_file.get_buffer('Topography')[0]
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.reconstruction.reconstruct[4]>", line 1, in <module>
        mi_buffer = mi_file.get_buffer('Topography')[0]
    NameError: name 'mi_file' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/reconstruction.py", line 202, in magni.afm.reconstruction.reconstruct
Failed example:
    mi_data = mi_buffer.get_data()
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.reconstruction.reconstruct[5]>", line 1, in <module>
        mi_data = mi_buffer.get_data()
    NameError: name 'mi_buffer' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/reconstruction.py", line 203, in magni.afm.reconstruction.reconstruct
Failed example:
    x = magni.imaging.mat2vec(mi_data)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.reconstruction.reconstruct[6]>", line 1, in <module>
        x = magni.imaging.mat2vec(mi_data)
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/reconstruction.py", line 216, in magni.afm.reconstruction.reconstruct
Failed example:
    Phi = magni.utils.matrices.Matrix(Phi_A, Phi_T, (),
                                      (int(len(x) / 2), len(x)))
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.reconstruction.reconstruct[9]>", line 1, in <module>
        Phi = magni.utils.matrices.Matrix(Phi_A, Phi_T, (),
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/reconstruction.py", line 222, in magni.afm.reconstruction.reconstruct
Failed example:
    Psi = magni.imaging.dictionaries.get_DCT(mi_data.shape)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.reconstruction.reconstruct[10]>", line 1, in <module>
        Psi = magni.imaging.dictionaries.get_DCT(mi_data.shape)
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/reconstruction.py", line 226, in magni.afm.reconstruction.reconstruct
Failed example:
    y = Phi.dot(x)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.reconstruction.reconstruct[11]>", line 1, in <module>
        y = Phi.dot(x)
    NameError: name 'Phi' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/reconstruction.py", line 227, in magni.afm.reconstruction.reconstruct
Failed example:
    print('Maximum absolute pixel error: {:.3f}'
          .format(np.abs(reconstruct(y, Phi, Psi) - x).max()))
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.reconstruction.reconstruct[12]>", line 2, in <module>
        .format(np.abs(reconstruct(y, Phi, Psi) - x).max()))
    NameError: name 'y' is not defined


======================================================================
FAIL: Doctest: magni.afm.types.Buffer
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib64/python3.3/doctest.py", line 2179, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for magni.afm.types.Buffer
  File "/.../magni/afm/types.py", line 35, in Buffer

----------------------------------------------------------------------
File "/.../magni/afm/types.py", line 62, in magni.afm.types.Buffer
Failed example:
    path = magni.utils.split_path(magni.__path__[0])[0]
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.types.Buffer[0]>", line 1, in <module>
        path = magni.utils.split_path(magni.__path__[0])[0]
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/types.py", line 63, in magni.afm.types.Buffer
Failed example:
    path = path + 'examples' + os.sep + 'example.mi'
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.types.Buffer[1]>", line 1, in <module>
        path = path + 'examples' + os.sep + 'example.mi'
    NameError: name 'path' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/types.py", line 64, in magni.afm.types.Buffer
Failed example:
    mi_file = magni.afm.io.read_mi_file(path)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.types.Buffer[2]>", line 1, in <module>
        mi_file = magni.afm.io.read_mi_file(path)
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/types.py", line 65, in magni.afm.types.Buffer
Failed example:
    mi_buffer = mi_file.get_buffer()[0]
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.types.Buffer[3]>", line 1, in <module>
        mi_buffer = mi_file.get_buffer()[0]
    NameError: name 'mi_file' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/types.py", line 70, in magni.afm.types.Buffer
Failed example:
    print(mi_buffer.get_attr('bufferLabel'))
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.types.Buffer[4]>", line 1, in <module>
        print(mi_buffer.get_attr('bufferLabel'))
    NameError: name 'mi_buffer' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/types.py", line 76, in magni.afm.types.Buffer
Failed example:
    data = mi_buffer.get_data()
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.types.Buffer[5]>", line 1, in <module>
        data = mi_buffer.get_data()
    NameError: name 'mi_buffer' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/types.py", line 77, in magni.afm.types.Buffer
Failed example:
    print('Buffer, Type: {}, Shape: {}'.format(str(type(data))[-15:-2],
    data.shape))
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.types.Buffer[6]>", line 1, in <module>
        print('Buffer, Type: {}, Shape: {}'.format(str(type(data))[-15:-2],
    NameError: name 'data' is not defined


======================================================================
FAIL: Doctest: magni.afm.types.Image
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib64/python3.3/doctest.py", line 2179, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for magni.afm.types.Image
  File "/.../magni/afm/types.py", line 199, in Image

----------------------------------------------------------------------
File "/.../magni/afm/types.py", line 222, in magni.afm.types.Image
Failed example:
    path = magni.utils.split_path(magni.__path__[0])[0]
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.types.Image[0]>", line 1, in <module>
        path = magni.utils.split_path(magni.__path__[0])[0]
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/types.py", line 223, in magni.afm.types.Image
Failed example:
    path = path + 'examples' + os.sep + 'example.mi'
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.types.Image[1]>", line 1, in <module>
        path = path + 'examples' + os.sep + 'example.mi'
    NameError: name 'path' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/types.py", line 224, in magni.afm.types.Image
Failed example:
    image = magni.afm.io.read_mi_file(path)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.types.Image[2]>", line 1, in <module>
        image = magni.afm.io.read_mi_file(path)
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/types.py", line 229, in magni.afm.types.Image
Failed example:
    print('{:5.2f}'.format(image.get_attr('scanSpeed')))
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.types.Image[3]>", line 1, in <module>
        print('{:5.2f}'.format(image.get_attr('scanSpeed')))
    NameError: name 'image' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/types.py", line 235, in magni.afm.types.Image
Failed example:
    buffers = image.get_buffer()
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.types.Image[4]>", line 1, in <module>
        buffers = image.get_buffer()
    NameError: name 'image' is not defined
----------------------------------------------------------------------
File "/.../magni/afm/types.py", line 236, in magni.afm.types.Image
Failed example:
    for b in buffers[0:5:2]:
        print('Buffer: {}'.format(b.get_attr('bufferLabel')))
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.afm.types.Image[5]>", line 1, in <module>
        for b in buffers[0:5:2]:
    NameError: name 'buffers' is not defined


======================================================================
FAIL: Doctest: magni.imaging.dictionaries.get_DCT
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib64/python3.3/doctest.py", line 2179, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for magni.imaging.dictionaries.get_DCT
  File "/.../magni/imaging/dictionaries.py", line 47, in get_DCT

----------------------------------------------------------------------
File "/.../magni/imaging/dictionaries.py", line 69, in magni.imaging.dictionaries.get_DCT
Failed example:
    img = np.random.randn(64, 64)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.dictionaries.get_DCT[0]>", line 1, in <module>
        img = np.random.randn(64, 64)
    NameError: name 'np' is not defined
----------------------------------------------------------------------
File "/.../magni/imaging/dictionaries.py", line 70, in magni.imaging.dictionaries.get_DCT
Failed example:
    vec = magni.imaging.mat2vec(img)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.dictionaries.get_DCT[1]>", line 1, in <module>
        vec = magni.imaging.mat2vec(img)
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/imaging/dictionaries.py", line 74, in magni.imaging.dictionaries.get_DCT
Failed example:
    dct_normal = magni.imaging._fastops.dct2(vec, *img.shape)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.dictionaries.get_DCT[2]>", line 1, in <module>
        dct_normal = magni.imaging._fastops.dct2(vec, *img.shape)
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/imaging/dictionaries.py", line 79, in magni.imaging.dictionaries.get_DCT
Failed example:
    matrix = get_DCT(img.shape)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.dictionaries.get_DCT[4]>", line 1, in <module>
        matrix = get_DCT(img.shape)
    NameError: name 'img' is not defined
----------------------------------------------------------------------
File "/.../magni/imaging/dictionaries.py", line 80, in magni.imaging.dictionaries.get_DCT
Failed example:
    dct_matrix = matrix.T.dot(vec)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.dictionaries.get_DCT[5]>", line 1, in <module>
        dct_matrix = matrix.T.dot(vec)
    NameError: name 'matrix' is not defined
----------------------------------------------------------------------
File "/.../magni/imaging/dictionaries.py", line 84, in magni.imaging.dictionaries.get_DCT
Failed example:
    np.allclose(dct_matrix, dct_normal)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.dictionaries.get_DCT[6]>", line 1, in <module>
        np.allclose(dct_matrix, dct_normal)
    NameError: name 'np' is not defined


======================================================================
FAIL: Doctest: magni.imaging.dictionaries.get_DFT
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib64/python3.3/doctest.py", line 2179, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for magni.imaging.dictionaries.get_DFT
  File "/.../magni/imaging/dictionaries.py", line 111, in get_DFT

----------------------------------------------------------------------
File "/.../magni/imaging/dictionaries.py", line 133, in magni.imaging.dictionaries.get_DFT
Failed example:
    img = np.random.randn(64, 64)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.dictionaries.get_DFT[0]>", line 1, in <module>
        img = np.random.randn(64, 64)
    NameError: name 'np' is not defined
----------------------------------------------------------------------
File "/.../magni/imaging/dictionaries.py", line 134, in magni.imaging.dictionaries.get_DFT
Failed example:
    vec = magni.imaging.mat2vec(img)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.dictionaries.get_DFT[1]>", line 1, in <module>
        vec = magni.imaging.mat2vec(img)
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/imaging/dictionaries.py", line 138, in magni.imaging.dictionaries.get_DFT
Failed example:
    dft_normal = magni.imaging._fastops.dft2(vec, *img.shape)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.dictionaries.get_DFT[2]>", line 1, in <module>
        dft_normal = magni.imaging._fastops.dft2(vec, *img.shape)
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/imaging/dictionaries.py", line 143, in magni.imaging.dictionaries.get_DFT
Failed example:
    matrix = get_DFT(img.shape)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.dictionaries.get_DFT[4]>", line 1, in <module>
        matrix = get_DFT(img.shape)
    NameError: name 'img' is not defined
----------------------------------------------------------------------
File "/.../magni/imaging/dictionaries.py", line 144, in magni.imaging.dictionaries.get_DFT
Failed example:
    dft_matrix = matrix.T.dot(vec)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.dictionaries.get_DFT[5]>", line 1, in <module>
        dft_matrix = matrix.T.dot(vec)
    NameError: name 'matrix' is not defined
----------------------------------------------------------------------
File "/.../magni/imaging/dictionaries.py", line 148, in magni.imaging.dictionaries.get_DFT
Failed example:
    np.allclose(dft_matrix, dft_normal)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.dictionaries.get_DFT[6]>", line 1, in <module>
        np.allclose(dft_matrix, dft_normal)
    NameError: name 'np' is not defined


======================================================================
FAIL: Doctest: magni.imaging.domains.MultiDomainImage
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib64/python3.3/doctest.py", line 2179, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for magni.imaging.domains.MultiDomainImage
  File "/.../magni/imaging/domains.py", line 24, in MultiDomainImage

----------------------------------------------------------------------
File "/.../magni/imaging/domains.py", line 54, in magni.imaging.domains.MultiDomainImage
Failed example:
    Phi = magni.utils.matrices.Matrix(func, func_T, (), (2, 3))
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.domains.MultiDomainImage[2]>", line 1, in <module>
        Phi = magni.utils.matrices.Matrix(func, func_T, (), (2, 3))
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/imaging/domains.py", line 58, in magni.imaging.domains.MultiDomainImage
Failed example:
    v = np.sqrt(0.5)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.domains.MultiDomainImage[3]>", line 1, in <module>
        v = np.sqrt(0.5)
    NameError: name 'np' is not defined
----------------------------------------------------------------------
File "/.../magni/imaging/domains.py", line 59, in magni.imaging.domains.MultiDomainImage
Failed example:
    Psi = np.float64([[ v, -v,  0],
                      [ v,  v,  0],
                      [ 0,  0,  1]])
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.domains.MultiDomainImage[4]>", line 1, in <module>
        Psi = np.float64([[ v, -v,  0],
    NameError: name 'np' is not defined
----------------------------------------------------------------------
File "/.../magni/imaging/domains.py", line 66, in magni.imaging.domains.MultiDomainImage
Failed example:
    domains = MultiDomainImage(Phi, Psi)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.domains.MultiDomainImage[6]>", line 1, in <module>
        domains = MultiDomainImage(Phi, Psi)
    NameError: name 'Phi' is not defined
----------------------------------------------------------------------
File "/.../magni/imaging/domains.py", line 71, in magni.imaging.domains.MultiDomainImage
Failed example:
    domains.image = np.ones(3).reshape(3, 1)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.domains.MultiDomainImage[7]>", line 1, in <module>
        domains.image = np.ones(3).reshape(3, 1)
    NameError: name 'np' is not defined
----------------------------------------------------------------------
File "/.../magni/imaging/domains.py", line 75, in magni.imaging.domains.MultiDomainImage
Failed example:
    domains.measurements
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.domains.MultiDomainImage[8]>", line 1, in <module>
        domains.measurements
    NameError: name 'domains' is not defined
----------------------------------------------------------------------
File "/.../magni/imaging/domains.py", line 81, in magni.imaging.domains.MultiDomainImage
Failed example:
    domains.coefficients
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.domains.MultiDomainImage[9]>", line 1, in <module>
        domains.coefficients
    NameError: name 'domains' is not defined


======================================================================
FAIL: Doctest: magni.imaging.measurements.construct_measurement_matrix
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib64/python3.3/doctest.py", line 2179, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for magni.imaging.measurements.construct_measurement_matrix
  File "/.../magni/imaging/measurements.py", line 130, in construct_measurement_matrix

----------------------------------------------------------------------
File "/.../magni/imaging/measurements.py", line 160, in magni.imaging.measurements.construct_measurement_matrix
Failed example:
    vec = magni.imaging.mat2vec(img)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.measurements.construct_measurement_matrix[1]>", line 1, in <module>
        vec = magni.imaging.mat2vec(img)
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/imaging/measurements.py", line 161, in magni.imaging.measurements.construct_measurement_matrix
Failed example:
    coords = magni.imaging.measurements.uniform_line_sample_image(
                 5, 5, 16., 17)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.measurements.construct_measurement_matrix[2]>", line 1, in <module>
        coords = magni.imaging.measurements.uniform_line_sample_image(
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/imaging/measurements.py", line 166, in magni.imaging.measurements.construct_measurement_matrix
Failed example:
    unique = magni.imaging.measurements.unique_pixels(coords)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.measurements.construct_measurement_matrix[3]>", line 1, in <module>
        unique = magni.imaging.measurements.unique_pixels(coords)
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/imaging/measurements.py", line 167, in magni.imaging.measurements.construct_measurement_matrix
Failed example:
    samples_normal = img[unique[:, 1], unique[:, 0]]
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.measurements.construct_measurement_matrix[4]>", line 1, in <module>
        samples_normal = img[unique[:, 1], unique[:, 0]]
    NameError: name 'unique' is not defined
----------------------------------------------------------------------
File "/.../magni/imaging/measurements.py", line 168, in magni.imaging.measurements.construct_measurement_matrix
Failed example:
    samples_normal = samples_normal.reshape((len(unique), 1))
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.measurements.construct_measurement_matrix[5]>", line 1, in <module>
        samples_normal = samples_normal.reshape((len(unique), 1))
    NameError: name 'samples_normal' is not defined
----------------------------------------------------------------------
File "/.../magni/imaging/measurements.py", line 173, in magni.imaging.measurements.construct_measurement_matrix
Failed example:
    matrix = construct_measurement_matrix(coords, *img.shape)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.measurements.construct_measurement_matrix[7]>", line 1, in <module>
        matrix = construct_measurement_matrix(coords, *img.shape)
    NameError: name 'coords' is not defined
----------------------------------------------------------------------
File "/.../magni/imaging/measurements.py", line 174, in magni.imaging.measurements.construct_measurement_matrix
Failed example:
    samples_matrix = matrix.dot(vec)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.measurements.construct_measurement_matrix[8]>", line 1, in <module>
        samples_matrix = matrix.dot(vec)
    NameError: name 'matrix' is not defined
----------------------------------------------------------------------
File "/.../magni/imaging/measurements.py", line 178, in magni.imaging.measurements.construct_measurement_matrix
Failed example:
    np.allclose(samples_matrix, samples_normal)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.imaging.measurements.construct_measurement_matrix[9]>", line 1, in <module>
        np.allclose(samples_matrix, samples_normal)
    NameError: name 'samples_matrix' is not defined


======================================================================
FAIL: Doctest: magni.imaging.preprocessing.detilt
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib64/python3.3/doctest.py", line 2179, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for magni.imaging.preprocessing.detilt
  File "/.../magni/imaging/preprocessing.py", line 46, in detilt

----------------------------------------------------------------------
File "/.../magni/imaging/preprocessing.py", line 99, in magni.imaging.preprocessing.detilt
Failed example:
    im
Expected:
    array([[  3.33333333e-01,  -3.33333333e-01,  -2.00000000e+00],
           [ -3.33333333e-01,   1.00000000e+00,   3.33333333e-01],
           [ -2.66453526e-15,   3.33333333e-01,  -3.33333333e-01]])
Got:
    array([[  3.33333333e-01,  -3.33333333e-01,  -2.00000000e+00],
           [ -3.33333333e-01,   1.00000000e+00,   3.33333333e-01],
           [  1.77635684e-15,   3.33333333e-01,  -3.33333333e-01]])


======================================================================
FAIL: Doctest: magni.reproducibility.io.annotate_database
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib64/python3.3/doctest.py", line 2179, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for magni.reproducibility.io.annotate_database
  File "/.../magni/reproducibility/io.py", line 55, in annotate_database

----------------------------------------------------------------------
File "/.../magni/reproducibility/io.py", line 94, in magni.reproducibility.io.annotate_database
Failed example:
    with magni.utils.multiprocessing.File('db.hdf5', mode='a') as h5file:
        annotate_database(h5file)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.reproducibility.io.annotate_database[1]>", line 1, in <module>
        with magni.utils.multiprocessing.File('db.hdf5', mode='a') as h5file:
    NameError: name 'magni' is not defined


======================================================================
FAIL: Doctest: magni.reproducibility.io.read_annotations
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib64/python3.3/doctest.py", line 2179, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for magni.reproducibility.io.read_annotations
  File "/.../magni/reproducibility/io.py", line 136, in read_annotations

----------------------------------------------------------------------
File "/.../magni/reproducibility/io.py", line 167, in magni.reproducibility.io.read_annotations
Failed example:
    with magni.utils.multiprocessing.File('db.hdf5', mode='r') as h5file:
       annotations = read_annotations(h5file)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.reproducibility.io.read_annotations[1]>", line 1, in <module>
        with magni.utils.multiprocessing.File('db.hdf5', mode='r') as h5file:
    NameError: name 'magni' is not defined


======================================================================
FAIL: Doctest: magni.reproducibility.io.remove_annotations
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib64/python3.3/doctest.py", line 2179, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for magni.reproducibility.io.remove_annotations
  File "/.../magni/reproducibility/io.py", line 209, in remove_annotations

----------------------------------------------------------------------
File "/.../magni/reproducibility/io.py", line 223, in magni.reproducibility.io.remove_annotations
Failed example:
    with magni.utils.multiprocessing.File('db.hdf5', mode='a') as h5file:
       remove_annotations(h5file)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.reproducibility.io.remove_annotations[1]>", line 1, in <module>
        with magni.utils.multiprocessing.File('db.hdf5', mode='a') as h5file:
    NameError: name 'magni' is not defined


======================================================================
FAIL: Doctest: magni.utils.matrices.MatrixCollection
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib64/python3.3/doctest.py", line 2179, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for magni.utils.matrices.MatrixCollection
  File "/.../magni/utils/matrices.py", line 228, in MatrixCollection

----------------------------------------------------------------------
File "/.../magni/utils/matrices.py", line 253, in magni.utils.matrices.MatrixCollection
Failed example:
    negate = magni.utils.matrices.Matrix(func, func, (), (3, 3))
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.utils.matrices.MatrixCollection[1]>", line 1, in <module>
        negate = magni.utils.matrices.Matrix(func, func, (), (3, 3))
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/utils/matrices.py", line 254, in magni.utils.matrices.MatrixCollection
Failed example:
    negate.A
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.utils.matrices.MatrixCollection[2]>", line 1, in <module>
        negate.A
    NameError: name 'negate' is not defined
----------------------------------------------------------------------
File "/.../magni/utils/matrices.py", line 262, in magni.utils.matrices.MatrixCollection
Failed example:
    reverse = magni.utils.matrices.Matrix(func, func, (), (3, 3))
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.utils.matrices.MatrixCollection[4]>", line 1, in <module>
        reverse = magni.utils.matrices.Matrix(func, func, (), (3, 3))
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/utils/matrices.py", line 263, in magni.utils.matrices.MatrixCollection
Failed example:
    reverse.A
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.utils.matrices.MatrixCollection[5]>", line 1, in <module>
        reverse.A
    NameError: name 'reverse' is not defined
----------------------------------------------------------------------
File "/.../magni/utils/matrices.py", line 271, in magni.utils.matrices.MatrixCollection
Failed example:
    matrix = MatrixCollection((negate, reverse))
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.utils.matrices.MatrixCollection[7]>", line 1, in <module>
        matrix = MatrixCollection((negate, reverse))
    NameError: name 'negate' is not defined
----------------------------------------------------------------------
File "/.../magni/utils/matrices.py", line 275, in magni.utils.matrices.MatrixCollection
Failed example:
    matrix.shape
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.utils.matrices.MatrixCollection[8]>", line 1, in <module>
        matrix.shape
    NameError: name 'matrix' is not defined
----------------------------------------------------------------------
File "/.../magni/utils/matrices.py", line 281, in magni.utils.matrices.MatrixCollection
Failed example:
    matrix.dot(vec)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.utils.matrices.MatrixCollection[10]>", line 1, in <module>
        matrix.dot(vec)
    NameError: name 'matrix' is not defined
----------------------------------------------------------------------
File "/.../magni/utils/matrices.py", line 289, in magni.utils.matrices.MatrixCollection
Failed example:
    matrix.A
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.utils.matrices.MatrixCollection[11]>", line 1, in <module>
        matrix.A
    NameError: name 'matrix' is not defined
----------------------------------------------------------------------
File "/.../magni/utils/matrices.py", line 296, in magni.utils.matrices.MatrixCollection
Failed example:
    matrix.T.A
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.utils.matrices.MatrixCollection[12]>", line 1, in <module>
        matrix.T.A
    NameError: name 'matrix' is not defined


======================================================================
FAIL: Doctest: magni.utils.plotting
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib64/python3.3/doctest.py", line 2179, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for magni.utils.plotting
  File "/.../magni/utils/plotting.py", line 0, in plotting

----------------------------------------------------------------------
File "/.../magni/utils/plotting.py", line 33, in magni.utils.plotting
Failed example:
    magni.utils.plotting.setup_matplotlib()
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.utils.plotting[0]>", line 1, in <module>
        magni.utils.plotting.setup_matplotlib()
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/utils/plotting.py", line 37, in magni.utils.plotting
Failed example:
    magni.utils.plotting.colour_collections['psp']['Blue']
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.utils.plotting[1]>", line 1, in <module>
        magni.utils.plotting.colour_collections['psp']['Blue']
    NameError: name 'magni' is not defined


======================================================================
FAIL: Doctest: magni.utils.validation.disable_validation
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib64/python3.3/doctest.py", line 2179, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for magni.utils.validation.disable_validation
  File "/.../magni/utils/validation.py", line 124, in disable_validation

----------------------------------------------------------------------
File "/.../magni/utils/validation.py", line 135, in magni.utils.validation.disable_validation
Failed example:
    @magni.utils.validation.decorate_validation
    def _validate_test(arg):
        magni.utils.validation.validate(arg, 'arg', {'type': int})
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest magni.utils.validation.disable_validation[0]>", line 1, in <module>
        @magni.utils.validation.decorate_validation
    NameError: name 'magni' is not defined
----------------------------------------------------------------------
File "/.../magni/utils/validation.py", line 155, in magni.utils.validation.disable_validation
Failed example:
    try:
        test('string')
        print('No exception occured')
    except BaseException:
        print('An exception occured')
Expected:
    No exception occured
Got:
    An exception occured


----------------------------------------------------------------------
Ran 43 tests in 5.640s

FAILED (failures=16)

Using doctest directly, some of these pass, but some of them still fail:

$ python3.3 -m doctest magni/afm/reconstruction.py
**********************************************************************
File "magni/afm/reconstruction.py", line 93, in reconstruction.analyse
Failed example:
    path = magni.utils.split_path(magni.__path__[0])[0]
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest reconstruction.analyse[1]>", line 1, in <module>
        path = magni.utils.split_path(magni.__path__[0])[0]
    NameError: name 'magni' is not defined
**********************************************************************
File "magni/afm/reconstruction.py", line 94, in reconstruction.analyse
Failed example:
    path = path + 'examples' + os.sep + 'example.mi'
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest reconstruction.analyse[2]>", line 1, in <module>
        path = path + 'examples' + os.sep + 'example.mi'
    NameError: name 'path' is not defined
**********************************************************************
File "magni/afm/reconstruction.py", line 95, in reconstruction.analyse
Failed example:
    mi_file = magni.afm.io.read_mi_file(path)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest reconstruction.analyse[3]>", line 1, in <module>
        mi_file = magni.afm.io.read_mi_file(path)
    NameError: name 'magni' is not defined
**********************************************************************
File "magni/afm/reconstruction.py", line 96, in reconstruction.analyse
Failed example:
    mi_buffer = mi_file.get_buffer('Topography')[0]
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest reconstruction.analyse[4]>", line 1, in <module>
        mi_buffer = mi_file.get_buffer('Topography')[0]
    NameError: name 'mi_file' is not defined
**********************************************************************
File "magni/afm/reconstruction.py", line 97, in reconstruction.analyse
Failed example:
    mi_data = mi_buffer.get_data()
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest reconstruction.analyse[5]>", line 1, in <module>
        mi_data = mi_buffer.get_data()
    NameError: name 'mi_buffer' is not defined
**********************************************************************
File "magni/afm/reconstruction.py", line 98, in reconstruction.analyse
Failed example:
    x = magni.imaging.mat2vec(mi_data)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest reconstruction.analyse[6]>", line 1, in <module>
        x = magni.imaging.mat2vec(mi_data)
    NameError: name 'magni' is not defined
**********************************************************************
File "magni/afm/reconstruction.py", line 111, in reconstruction.analyse
Failed example:
    Phi = magni.utils.matrices.Matrix(Phi_A, Phi_T, (),
                                      (int(len(x) / 2), len(x)))
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest reconstruction.analyse[9]>", line 1, in <module>
        Phi = magni.utils.matrices.Matrix(Phi_A, Phi_T, (),
    NameError: name 'magni' is not defined
**********************************************************************
File "magni/afm/reconstruction.py", line 117, in reconstruction.analyse
Failed example:
    Psi = magni.imaging.dictionaries.get_DCT(mi_data.shape)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest reconstruction.analyse[10]>", line 1, in <module>
        Psi = magni.imaging.dictionaries.get_DCT(mi_data.shape)
    NameError: name 'magni' is not defined
**********************************************************************
File "magni/afm/reconstruction.py", line 121, in reconstruction.analyse
Failed example:
    print('MSE: {:.2f}, PSNR: {:.2f}'.format(*analyse(x, Phi, Psi)))
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest reconstruction.analyse[11]>", line 1, in <module>
        print('MSE: {:.2f}, PSNR: {:.2f}'.format(*analyse(x, Phi, Psi)))
    NameError: name 'x' is not defined
**********************************************************************
File "magni/afm/reconstruction.py", line 198, in reconstruction.reconstruct
Failed example:
    path = magni.utils.split_path(magni.__path__[0])[0]
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest reconstruction.reconstruct[1]>", line 1, in <module>
        path = magni.utils.split_path(magni.__path__[0])[0]
    NameError: name 'magni' is not defined
**********************************************************************
File "magni/afm/reconstruction.py", line 199, in reconstruction.reconstruct
Failed example:
    path = path + 'examples' + os.sep + 'example.mi'
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest reconstruction.reconstruct[2]>", line 1, in <module>
        path = path + 'examples' + os.sep + 'example.mi'
    NameError: name 'path' is not defined
**********************************************************************
File "magni/afm/reconstruction.py", line 200, in reconstruction.reconstruct
Failed example:
    mi_file = magni.afm.io.read_mi_file(path)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest reconstruction.reconstruct[3]>", line 1, in <module>
        mi_file = magni.afm.io.read_mi_file(path)
    NameError: name 'magni' is not defined
**********************************************************************
File "magni/afm/reconstruction.py", line 201, in reconstruction.reconstruct
Failed example:
    mi_buffer = mi_file.get_buffer('Topography')[0]
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest reconstruction.reconstruct[4]>", line 1, in <module>
        mi_buffer = mi_file.get_buffer('Topography')[0]
    NameError: name 'mi_file' is not defined
**********************************************************************
File "magni/afm/reconstruction.py", line 202, in reconstruction.reconstruct
Failed example:
    mi_data = mi_buffer.get_data()
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest reconstruction.reconstruct[5]>", line 1, in <module>
        mi_data = mi_buffer.get_data()
    NameError: name 'mi_buffer' is not defined
**********************************************************************
File "magni/afm/reconstruction.py", line 203, in reconstruction.reconstruct
Failed example:
    x = magni.imaging.mat2vec(mi_data)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest reconstruction.reconstruct[6]>", line 1, in <module>
        x = magni.imaging.mat2vec(mi_data)
    NameError: name 'magni' is not defined
**********************************************************************
File "magni/afm/reconstruction.py", line 216, in reconstruction.reconstruct
Failed example:
    Phi = magni.utils.matrices.Matrix(Phi_A, Phi_T, (),
                                      (int(len(x) / 2), len(x)))
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest reconstruction.reconstruct[9]>", line 1, in <module>
        Phi = magni.utils.matrices.Matrix(Phi_A, Phi_T, (),
    NameError: name 'magni' is not defined
�[?1034h**********************************************************************
File "magni/afm/reconstruction.py", line 222, in reconstruction.reconstruct
Failed example:
    Psi = magni.imaging.dictionaries.get_DCT(mi_data.shape)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest reconstruction.reconstruct[10]>", line 1, in <module>
        Psi = magni.imaging.dictionaries.get_DCT(mi_data.shape)
    NameError: name 'magni' is not defined
**********************************************************************
File "magni/afm/reconstruction.py", line 226, in reconstruction.reconstruct
Failed example:
    y = Phi.dot(x)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest reconstruction.reconstruct[11]>", line 1, in <module>
        y = Phi.dot(x)
    NameError: name 'Phi' is not defined
**********************************************************************
File "magni/afm/reconstruction.py", line 227, in reconstruction.reconstruct
Failed example:
    print('Maximum absolute pixel error: {:.3f}'
          .format(np.abs(reconstruct(y, Phi, Psi) - x).max()))
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python3.3/doctest.py", line 1313, in __run
        compileflags, 1), test.globs)
      File "<doctest reconstruction.reconstruct[12]>", line 2, in <module>
        .format(np.abs(reconstruct(y, Phi, Psi) - x).max()))
    NameError: name 'y' is not defined
**********************************************************************
2 items had failures:
   9 of  12 in reconstruction.analyse
  10 of  13 in reconstruction.reconstruct
***Test Failed*** 19 failures.

Maybe I'm just invoking these wrong?

Validation of integer types raise exceptions when run on Windows

Integers and long integers are different types in Python 2 on Windows. This causes exceptions to be raised when the current type validation only allows integers and not long integers.

The issue causes the following examples to fail:

• imaging-dictionaries
• imaging-domains
• imaging-preprocessing
• magni

Some doctests fail when run on Windows due to expected integers being long integers

When run on Windows, Python 2 prints integer types as part of the value, e.g.:

>>> import numpy as np
>>> A = np.zeros((256, 256))
>>> print(A.shape)
(256L, 256L)

This results in 5 failed doctests in magni 1.0.0.

Furthermore, when run on Windows, Python (both 2 and 3) prints integer dtypes along with arrays, e.g.:

>>> import numpy as np
>>> print(np.arange(4, dtype=np.int64))
array([0, 1, 2, 3], dtype=int64)

This results in 1 failed doctest in magni 1.0.0.