test.py 18.9 KB
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#!/usr/bin/env python
# vim: set fileencoding=utf-8 :


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"""Unit tests against references extracted from

Matlab code from Bram Ton available on the matlab central website:

https://www.mathworks.com/matlabcentral/fileexchange/35754-wide-line-detector

This code implements the detector described in [HDLTL10] (see the references in
the generated sphinx documentation)
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"""

import os
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import numpy
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import numpy as np
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import nose.tools

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import pkg_resources

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import bob.io.base
import bob.io.matlab
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import bob.io.image
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from ..preprocessor import utils as preprocessor_utils
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def F(parts):
  """Returns the test file path"""

  return pkg_resources.resource_filename(__name__, os.path.join(*parts))
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def test_finger_crop():

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  input_filename = F(('preprocessors', '0019_3_1_120509-160517.png'))
  output_img_filename  = F(('preprocessors',
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    '0019_3_1_120509-160517_img_lee_huang.mat'))
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  output_fvr_filename  = F(('preprocessors',
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    '0019_3_1_120509-160517_fvr_lee_huang.mat'))

  img = bob.io.base.load(input_filename)

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  from bob.bio.vein.preprocessor.FingerCrop import FingerCrop
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  preprocess = FingerCrop(fingercontour='leemaskMatlab', padding_width=0)
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  preproc, mask = preprocess(img)
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  #preprocessor_utils.show_mask_over_image(preproc, mask)
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  mask_ref = bob.io.base.load(output_fvr_filename).astype('bool')
  preproc_ref = bob.core.convert(bob.io.base.load(output_img_filename),
      numpy.uint8, (0,255), (0.0,1.0))

  assert numpy.mean(numpy.abs(mask - mask_ref)) < 1e-2
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 # Very loose comparison!
  #preprocessor_utils.show_image(numpy.abs(preproc.astype('int16') - preproc_ref.astype('int16')).astype('uint8'))
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  assert numpy.mean(numpy.abs(preproc - preproc_ref)) < 1.3e2
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def test_max_curvature():
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  #Maximum Curvature method against Matlab reference

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  input_img_filename  = F(('extractors', 'miuramax_input_img.mat'))
  input_fvr_filename  = F(('extractors', 'miuramax_input_fvr.mat'))
  output_filename     = F(('extractors', 'miuramax_output.mat'))
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  # Load inputs
  input_img = bob.io.base.load(input_img_filename)
  input_fvr = bob.io.base.load(input_fvr_filename)

  # Apply Python implementation
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  from bob.bio.vein.extractor.MaximumCurvature import MaximumCurvature
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  MC = MaximumCurvature(5)
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  output_img = MC((input_img, input_fvr))

  # Load Matlab reference
  output_img_ref = bob.io.base.load(output_filename)

  # Compare output of python's implementation to matlab reference
  # (loose comparison!)
  assert numpy.mean(numpy.abs(output_img - output_img_ref)) < 8e-3
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def test_max_curvature_HE():
  # Maximum Curvature method when Histogram Equalization post-processing is applied to the preprocessed vein image

  # Read in input image
  input_img_filename = F(('preprocessors', '0019_3_1_120509-160517.png'))
  input_img = bob.io.base.load(input_img_filename)
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  # Preprocess the data and apply Histogram Equalization postprocessing (same parameters as in maximum_curvature.py configuration file + postprocessing)
  from bob.bio.vein.preprocessor.FingerCrop import FingerCrop
  FC = FingerCrop(postprocessing = 'HE')
  preproc_data = FC(input_img)

  # Extract features from preprocessed and histogram equalized data using MC extractor (same parameters as in maximum_curvature.py configuration file)
  from bob.bio.vein.extractor.MaximumCurvature import MaximumCurvature
  MC = MaximumCurvature(sigma = 5)
  extr_data = MC(preproc_data)


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def test_repeated_line_tracking():
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  #Repeated Line Tracking method against Matlab reference

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  input_img_filename  = F(('extractors', 'miurarlt_input_img.mat'))
  input_fvr_filename  = F(('extractors', 'miurarlt_input_fvr.mat'))
  output_filename     = F(('extractors', 'miurarlt_output.mat'))
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  # Load inputs
  input_img = bob.io.base.load(input_img_filename)
  input_fvr = bob.io.base.load(input_fvr_filename)

  # Apply Python implementation
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  from bob.bio.vein.extractor.RepeatedLineTracking import RepeatedLineTracking
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  RLT = RepeatedLineTracking(3000, 1, 21, False)
  output_img = RLT((input_img, input_fvr))

  # Load Matlab reference
  output_img_ref = bob.io.base.load(output_filename)

  # Compare output of python's implementation to matlab reference
  # (loose comparison!)
  assert numpy.mean(numpy.abs(output_img - output_img_ref)) < 0.5


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def test_repeated_line_tracking_HE():
  # Repeated Line Tracking method when Histogram Equalization post-processing is applied to the preprocessed vein image

  # Read in input image
  input_img_filename = F(('preprocessors', '0019_3_1_120509-160517.png'))
  input_img = bob.io.base.load(input_img_filename)
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  # Preprocess the data and apply Histogram Equalization postprocessing (same parameters as in repeated_line_tracking.py configuration file + postprocessing)
  from bob.bio.vein.preprocessor.FingerCrop import FingerCrop
  FC = FingerCrop(postprocessing = 'HE')
  preproc_data = FC(input_img)

  # Extract features from preprocessed and histogram equalized data using RLT extractor (same parameters as in repeated_line_tracking.py configuration file)
  from bob.bio.vein.extractor.RepeatedLineTracking import RepeatedLineTracking
  # Maximum number of iterations
  NUMBER_ITERATIONS = 3000
  # Distance between tracking point and cross section of profile
  DISTANCE_R = 1
  # Width of profile
  PROFILE_WIDTH = 21
  RLT = RepeatedLineTracking(iterations = NUMBER_ITERATIONS, r = DISTANCE_R, profile_w = PROFILE_WIDTH, seed = 0)
  extr_data = RLT(preproc_data)


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def test_wide_line_detector():
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  #Wide Line Detector method against Matlab reference

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  input_img_filename  = F(('extractors', 'huangwl_input_img.mat'))
  input_fvr_filename  = F(('extractors', 'huangwl_input_fvr.mat'))
  output_filename     = F(('extractors', 'huangwl_output.mat'))
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  # Load inputs
  input_img = bob.io.base.load(input_img_filename)
  input_fvr = bob.io.base.load(input_fvr_filename)

  # Apply Python implementation
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  from bob.bio.vein.extractor.WideLineDetector import WideLineDetector
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  WL = WideLineDetector(5, 1, 41, False)
  output_img = WL((input_img, input_fvr))

  # Load Matlab reference
  output_img_ref = bob.io.base.load(output_filename)

  # Compare output of python's implementation to matlab reference
  assert numpy.allclose(output_img, output_img_ref)


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def test_wide_line_detector_HE():
  # Wide Line Detector method when Histogram Equalization post-processing is applied to the preprocessed vein image

  # Read in input image
  input_img_filename = F(('preprocessors', '0019_3_1_120509-160517.png'))
  input_img = bob.io.base.load(input_img_filename)
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  # Preprocess the data and apply Histogram Equalization postprocessing (same parameters as in wide_line_detector.py configuration file + postprocessing)
  from bob.bio.vein.preprocessor.FingerCrop import FingerCrop
  FC = FingerCrop(postprocessing = 'HE')
  preproc_data = FC(input_img)

  # Extract features from preprocessed and histogram equalized data using WLD extractor (same parameters as in wide_line_detector.py configuration file)
  from bob.bio.vein.extractor.WideLineDetector import WideLineDetector
  # Radius of the circular neighbourhood region
  RADIUS_NEIGHBOURHOOD_REGION = 5
  NEIGHBOURHOOD_THRESHOLD = 1
  # Sum of neigbourhood threshold
  SUM_NEIGHBOURHOOD = 41
  RESCALE = True
  WLD = WideLineDetector(radius = RADIUS_NEIGHBOURHOOD_REGION, threshold = NEIGHBOURHOOD_THRESHOLD, g = SUM_NEIGHBOURHOOD, rescale = RESCALE)
  extr_data = WLD(preproc_data)


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def test_miura_match():

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  #Match Ratio method against Matlab reference

  template_filename = F(('algorithms', '0001_2_1_120509-135338.mat'))
  probe_gen_filename = F(('algorithms', '0001_2_2_120509-135558.mat'))
  probe_imp_filename = F(('algorithms', '0003_2_1_120509-141255.mat'))
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  template_vein = bob.io.base.load(template_filename)
  probe_gen_vein = bob.io.base.load(probe_gen_filename)
  probe_imp_vein = bob.io.base.load(probe_imp_filename)

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  from bob.bio.vein.algorithm.MiuraMatch import MiuraMatch
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  MM = MiuraMatch(ch=18, cw=28)
  score_gen = MM.score(template_vein, probe_gen_vein)

  assert numpy.isclose(score_gen, 0.382689335394127)

  score_imp = MM.score(template_vein, probe_imp_vein)
  assert numpy.isclose(score_imp, 0.172906739278421)
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def test_assert_points():

  # Tests that point assertion works as expected
  area = (10, 5)
  inside = [(0,0), (3,2), (9, 4)]
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  preprocessor_utils.assert_points(area, inside) #should not raise
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  def _check_outside(point):
    # should raise, otherwise it is an error
    try:
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      preprocessor_utils.assert_points(area, [point])
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    except AssertionError as e:
      assert str(point) in str(e)
    else:
      raise AssertionError("Did not assert %s is outside of %s" % (point, area))

  outside = [(-1, 0), (10, 0), (0, 5), (10, 5), (15,12)]
  for k in outside: _check_outside(k)


def test_fix_points():

  # Tests that point clipping works as expected
  area = (10, 5)
  inside = [(0,0), (3,2), (9, 4)]
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  fixed = preprocessor_utils.fix_points(area, inside)
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  assert numpy.array_equal(inside, fixed), '%r != %r' % (inside, fixed)

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  fixed = preprocessor_utils.fix_points(area, [(-1, 0)])
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  assert numpy.array_equal(fixed, [(0, 0)])

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  fixed = preprocessor_utils.fix_points(area, [(10, 0)])
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  assert numpy.array_equal(fixed, [(9, 0)])

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  fixed = preprocessor_utils.fix_points(area, [(0, 5)])
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  assert numpy.array_equal(fixed, [(0, 4)])

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  fixed = preprocessor_utils.fix_points(area, [(10, 5)])
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  assert numpy.array_equal(fixed, [(9, 4)])

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  fixed = preprocessor_utils.fix_points(area, [(15, 12)])
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  assert numpy.array_equal(fixed, [(9, 4)])


def test_poly_to_mask():

  # Tests we can generate a mask out of a polygon correctly
  area = (10, 9) #10 rows, 9 columns
  polygon = [(2, 2), (2, 7), (7, 7), (7, 2)] #square shape, (y, x) format
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  mask = preprocessor_utils.poly_to_mask(area, polygon)
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  nose.tools.eq_(mask.dtype, numpy.bool)

  # This should be the output:
  expected = numpy.array([
      [False, False, False, False, False, False, False, False, False],
      [False, False, False, False, False, False, False, False, False],
      [False, False, True,  True,  True,  True,  True,  True,  False],
      [False, False, True,  True,  True,  True,  True,  True,  False],
      [False, False, True,  True,  True,  True,  True,  True,  False],
      [False, False, True,  True,  True,  True,  True,  True,  False],
      [False, False, True,  True,  True,  True,  True,  True,  False],
      [False, False, True,  True,  True,  True,  True,  True,  False],
      [False, False, False, False, False, False, False, False, False],
      [False, False, False, False, False, False, False, False, False],
      ])
  assert numpy.array_equal(mask, expected)

  polygon = [(3, 2), (5, 7), (8, 7), (7, 3)] #trapezoid, (y, x) format
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  mask = preprocessor_utils.poly_to_mask(area, polygon)
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  nose.tools.eq_(mask.dtype, numpy.bool)

  # This should be the output:
  expected = numpy.array([
      [False, False, False, False, False, False, False, False, False],
      [False, False, False, False, False, False, False, False, False],
      [False, False, False, False, False, False, False, False, False],
      [False, False, True,  False, False, False, False, False, False],
      [False, False, True,  True,  True,  False, False, False, False],
      [False, False, False, True,  True,  True,  True,  True,  False],
      [False, False, False, True,  True,  True,  True,  True,  False],
      [False, False, False, True,  True,  True,  True,  True,  False],
      [False, False, False, False, False, False, False, True,  False],
      [False, False, False, False, False, False, False, False, False],
      ])
  assert numpy.array_equal(mask, expected)


def test_mask_to_image():

  # Tests we can correctly convert a boolean array into an image
  # that makes sense according to the data types
  sample = numpy.array([False, True])
  nose.tools.eq_(sample.dtype, numpy.bool)

  def _check_uint(n):
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    conv = preprocessor_utils.mask_to_image(sample, 'uint%d' % n)
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    nose.tools.eq_(conv.dtype, getattr(numpy, 'uint%d' % n))
    target = [0, (2**n)-1]
    assert numpy.array_equal(conv, target), '%r != %r' % (conv, target)

  _check_uint(8)
  _check_uint(16)
  _check_uint(32)
  _check_uint(64)

  def _check_float(n):
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    conv = preprocessor_utils.mask_to_image(sample, 'float%d' % n)
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    nose.tools.eq_(conv.dtype, getattr(numpy, 'float%d' % n))
    assert numpy.array_equal(conv, [0, 1.0]), '%r != %r' % (conv, target)

  _check_float(32)
  _check_float(64)
  _check_float(128)


  # This should be unsupported
  try:
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    conv = preprocessor_utils.mask_to_image(sample, 'int16')
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  except TypeError as e:
    assert 'int16' in str(e)
  else:
    raise AssertionError('Conversion to int16 did not trigger a TypeError')
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def test_jaccard_index():

  # Tests to verify the Jaccard index calculation is accurate
  a = numpy.array([
    [False, False],
    [True, True],
    ])

  b = numpy.array([
    [True, True],
    [True, False],
    ])

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  nose.tools.eq_(preprocessor_utils.jaccard_index(a, b), 1.0/4.0)
  nose.tools.eq_(preprocessor_utils.jaccard_index(a, a), 1.0)
  nose.tools.eq_(preprocessor_utils.jaccard_index(b, b), 1.0)
  nose.tools.eq_(preprocessor_utils.jaccard_index(a, numpy.ones(a.shape, dtype=bool)), 2.0/4.0)
  nose.tools.eq_(preprocessor_utils.jaccard_index(a, numpy.zeros(a.shape, dtype=bool)), 0.0)
  nose.tools.eq_(preprocessor_utils.jaccard_index(b, numpy.ones(b.shape, dtype=bool)), 3.0/4.0)
  nose.tools.eq_(preprocessor_utils.jaccard_index(b, numpy.zeros(b.shape, dtype=bool)), 0.0)
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def test_intersection_ratio():

  # Tests to verify the intersection ratio calculation is accurate
  a = numpy.array([
    [False, False],
    [True, True],
    ])

  b = numpy.array([
    [True, False],
    [True, False],
    ])

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  nose.tools.eq_(preprocessor_utils.intersect_ratio(a, b), 1.0/2.0)
  nose.tools.eq_(preprocessor_utils.intersect_ratio(a, a), 1.0)
  nose.tools.eq_(preprocessor_utils.intersect_ratio(b, b), 1.0)
  nose.tools.eq_(preprocessor_utils.intersect_ratio(a, numpy.ones(a.shape, dtype=bool)), 1.0)
  nose.tools.eq_(preprocessor_utils.intersect_ratio(a, numpy.zeros(a.shape, dtype=bool)), 0)
  nose.tools.eq_(preprocessor_utils.intersect_ratio(b, numpy.ones(b.shape, dtype=bool)), 1.0)
  nose.tools.eq_(preprocessor_utils.intersect_ratio(b, numpy.zeros(b.shape, dtype=bool)), 0)

  nose.tools.eq_(preprocessor_utils.intersect_ratio_of_complement(a, b), 1.0/2.0)
  nose.tools.eq_(preprocessor_utils.intersect_ratio_of_complement(a, a), 0.0)
  nose.tools.eq_(preprocessor_utils.intersect_ratio_of_complement(b, b), 0.0)
  nose.tools.eq_(preprocessor_utils.intersect_ratio_of_complement(a, numpy.ones(a.shape, dtype=bool)), 1.0)
  nose.tools.eq_(preprocessor_utils.intersect_ratio_of_complement(a, numpy.zeros(a.shape, dtype=bool)), 0)
  nose.tools.eq_(preprocessor_utils.intersect_ratio_of_complement(b, numpy.ones(b.shape, dtype=bool)), 1.0)
  nose.tools.eq_(preprocessor_utils.intersect_ratio_of_complement(b, numpy.zeros(b.shape, dtype=bool)), 0)


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def test_correlation():
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  # A test for convolution performance. Correlations are used on the Miura
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  # Match algorithm, therefore we want to make sure we can perform them as fast
  # as possible.
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  import numpy
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  import scipy.signal
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  import bob.sp
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  # Rough example from Vera fingervein database
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  Y = 250
  X = 600
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  CH = 80
  CW = 90
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  def gen_ab():
    a = numpy.random.randint(256, size=(Y, X)).astype(float)
    b = numpy.random.randint(256, size=(Y-CH, X-CW)).astype(float)
    return a, b

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  def bob_function(a, b):

    # rotate input image by 180 degrees
    b = numpy.rot90(b, k=2)

    # Determine padding size in x and y dimension
    size_a  = numpy.array(a.shape)
    size_b  = numpy.array(b.shape)
    outsize = size_a + size_b - 1

    # Determine 2D cross correlation in Fourier domain
    a2 = numpy.zeros(outsize)
    a2[0:size_a[0],0:size_a[1]] = a
    Fa = bob.sp.fft(a2.astype(numpy.complex128))

    b2 = numpy.zeros(outsize)
    b2[0:size_b[0],0:size_b[1]] = b
    Fb = bob.sp.fft(b2.astype(numpy.complex128))

    conv_ab = numpy.real(bob.sp.ifft(Fa*Fb))

    h, w = size_a - size_b + 1

    Nm = conv_ab[size_b[0]-1:size_b[0]-1+h, size_b[1]-1:size_b[1]-1+w]

    t0, s0 = numpy.unravel_index(Nm.argmax(), Nm.shape)

    # this is our output
    Nmm = Nm[t0,s0]

    # normalizes the output by the number of pixels lit on the input
    # matrices, taking into consideration the surface that produced the
    # result (i.e., the eroded model and part of the probe)
    h, w = b.shape
    return Nmm/(sum(sum(b)) + sum(sum(a[t0:t0+h-2*CH, s0:s0+w-2*CW])))

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  def scipy_function(a, b):
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    b = numpy.rot90(b, k=2)

    Nm = scipy.signal.convolve2d(a, b, 'valid')

    # figures out where the maximum is on the resulting matrix
    t0, s0 = numpy.unravel_index(Nm.argmax(), Nm.shape)

    # this is our output
    Nmm = Nm[t0,s0]

    # normalizes the output by the number of pixels lit on the input
    # matrices, taking into consideration the surface that produced the
    # result (i.e., the eroded model and part of the probe)
    h, w = b.shape
    return Nmm/(sum(sum(b)) + sum(sum(a[t0:t0+h-2*CH, s0:s0+w-2*CW])))

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  def scipy2_function(a, b):
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    b = numpy.rot90(b, k=2)
    Nm = scipy.signal.fftconvolve(a, b, 'valid')

    # figures out where the maximum is on the resulting matrix
    t0, s0 = numpy.unravel_index(Nm.argmax(), Nm.shape)

    # this is our output
    Nmm = Nm[t0,s0]

    # normalizes the output by the number of pixels lit on the input
    # matrices, taking into consideration the surface that produced the
    # result (i.e., the eroded model and part of the probe)
    h, w = b.shape
    return Nmm/(sum(sum(b)) + sum(sum(a[t0:t0+h-2*CH, s0:s0+w-2*CW])))


  def scipy3_function(a, b):
    Nm = scipy.signal.correlate2d(a, b, 'valid')

    # figures out where the maximum is on the resulting matrix
    t0, s0 = numpy.unravel_index(Nm.argmax(), Nm.shape)

    # this is our output
    Nmm = Nm[t0,s0]

    # normalizes the output by the number of pixels lit on the input
    # matrices, taking into consideration the surface that produced the
    # result (i.e., the eroded model and part of the probe)
    h, w = b.shape
    return Nmm/(sum(sum(b)) + sum(sum(a[t0:t0+h-2*CH, s0:s0+w-2*CW])))
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  a, b = gen_ab()
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  assert numpy.allclose(bob_function(a, b), scipy_function(a, b))
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  assert numpy.allclose(scipy_function(a, b), scipy2_function(a, b))
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  assert numpy.allclose(scipy2_function(a, b), scipy3_function(a, b))
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  # if you want to test timings, uncomment the following section
  '''
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  import time

  start = time.clock()
  N = 10
  for i in range(N):
    a, b = gen_ab()
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    bob_function(a, b)
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  total = time.clock() - start
523
  print('bob implementation, %d iterations - %.2e per iteration' % (N, total/N))
524 525 526 527 528 529

  start = time.clock()
  for i in range(N):
    a, b = gen_ab()
    scipy_function(a, b)
  total = time.clock() - start
530
  print('scipy+convolve, %d iterations - %.2e per iteration' % (N, total/N))
531 532 533 534 535 536

  start = time.clock()
  for i in range(N):
    a, b = gen_ab()
    scipy2_function(a, b)
  total = time.clock() - start
537 538 539 540 541 542 543 544 545
  print('scipy+fftconvolve, %d iterations - %.2e per iteration' % (N, total/N))

  start = time.clock()
  for i in range(N):
    a, b = gen_ab()
    scipy3_function(a, b)
  total = time.clock() - start
  print('scipy+correlate2d, %d iterations - %.2e per iteration' % (N, total/N))
  '''