Merge pull request #28 from hoechenberger/image-utils

Add some image processing

CHANGES.rst

@@ -2,7 +2,7 @@
 Changelog
 =========
 ****************
-v0.4, 2014-11-24
+v0.5, 2014-XX-XX
 ****************
 - ``compare_*`` functions renamed to ``gen_*``.
 - ``get_cdf*`` functions renamed to ``get_percentiles*``.
@@ -11,6 +11,7 @@ v0.4, 2014-11-24
 - Add sum_cdfs() to calculate the sum of an arbitrary number of CDFs.
 - Remove plotting functionality.
 - gen_cdf() completely reworked to be more readable and faster (>2x).
+- Add ``image`` module
 
 ******************
 v0.3.1, 2014-09-01

pphelper/__init__.py

@@ -7,6 +7,6 @@
 """
 
 from .version import __version__
-from . import racemodel, hardware
+from . import racemodel, hardware, utils, image
 
-__all__ = ['racemodel', 'hardware', 'utils']
+__all__ = ['racemodel', 'hardware', 'utils', 'image']

pphelper/image.py

@@ -0,0 +1,94 @@
+# -*- coding: utf-8 -*-
+
+"""
+pphelper.image
+==================
+
+Provides
+--------
+ - ``fft_image`` : Perform an FFT on the supplied image array.
+ - ``lowpass_filter_image`` : Load an image from a file, and low-pass
+                              filter via a Gaussian kernel.
+
+"""
+
+from __future__ import unicode_literals
+
+from collections import namedtuple
+import numpy as np
+from scipy.misc import imread
+from scipy import ndimage
+import pyfftw
+from pyfftw.interfaces.scipy_fftpack import fft2
+
+# Enable cache for FFTW to speed up calculations
+pyfftw.interfaces.cache.enable()
+pyfftw.interfaces.cache.set_keepalive_time(60)
+
+
+def fft_image(image):
+    """
+    Perform an FFT on the supplied image array.
+
+    Parameters
+    ----------
+    image : ndarray
+        An array of the image
+
+    Returns
+    -------
+    namedtuple
+        A namedtuple containing the the fast-fourier transform, the
+        amplitude and phase.
+
+    """
+    image_fft = fft2(image)
+    image_amplitude = np.abs(image_fft)
+    image_phase = np.angle(image_fft)
+
+    result = namedtuple('Image', 'FFT Amplitude Phase')
+    return result(image_fft, image_amplitude, image_phase)
+
+
+def lowpass_filter_image(image=None, filename=None, flatten=False,
+                         sigma=3):
+    """
+    Load an image from a file, and low-pass filter via a Gaussian kernel.
+
+    Parameters
+    ----------
+    image : ndarray, optional
+        The image to be processed. This will usually have been created
+        using `scipy.misc.imread` or a similar function.
+        If this argument is present, `filename` will be ignored.
+
+    filename : string, optional
+        The name of the image file to load and process.
+        Will be ignored is `image_array` is not `None`.
+
+    flatten : bool, optional
+        Whether to "flatten" the image before filtering,
+        i.e. convert it to grayscale.
+
+    sigma : scalar, optional
+        The standard deviation for Gaussian kernel.
+        See `scipy.ndimage.filters.gaussian_filter`.
+
+    Returns
+    -------
+    ndarray
+        The lowpass-filtered image.
+
+    See Also
+    --------
+    scipy.ndimage.gaussian_filter
+
+    """
+    if (image is None) and (filename is None):
+        raise AttributeError('Please supply either an image array or an'
+                             'image filename in lowpass_filter_image().')
+
+    if image is None:
+        image = imread(filename, flatten=flatten)
+
+    return ndimage.gaussian_filter(image, sigma)

pphelper/tests/data/fftw3-wisdom.pickle

@@ -0,0 +1,8 @@
+(S'(fftw-3.3.3 fftw_wisdom #x3c273403 #x192df114 #x4d08727c #xe98e9b9d\n)\n'
+p0
+S'(fftw-3.3.3 fftwf_wisdom #x706526c0 #x2f8b6c85 #x8cd1bb1a #x7c96e03d\n  (fftwf_dft_vrank_geq1_register 0 #x10bdd #x10bdd #x0 #x944f503b #xf8534f89 #x76809261 #x52b8aecd)\n  (fftwf_codelet_t1fuv_2_sse2 0 #x10bdd #x10bdd #x0 #x2cee21a0 #xfbab248b #x058f86de #xf548f89a)\n  (fftwf_codelet_t1fuv_5_sse2 0 #x11bdd #x11bdd #x0 #x1b82f8d3 #x717fb11c #xb27d7e69 #x03ff8807)\n  (fftwf_dft_buffered_register 1 #x11bdd #x11bdd #x0 #xd712df88 #x3ee16826 #x2b7042c8 #x46362a36)\n  (fftwf_dft_vrank_geq1_register 0 #x10bdd #x10bdd #x0 #xa6e0da61 #xa6dac649 #x375a536c #xb237dc8b)\n  (fftwf_dft_r2hc_register 0 #x10bdd #x10bdd #x0 #x2cbe16c0 #x7ddb4319 #x7340c78f #x68f0b812)\n  (fftwf_dft_vrank_geq1_register 0 #x11bdd #x11bdd #x0 #x427ecc38 #xcf08e4d1 #xc19d2ad5 #xc87a901e)\n  (fftwf_rdft_rank0_register 0 #x10bdd #x10bdd #x0 #xf07fa2f8 #x81ccc2cf #xbe2f3774 #xebc07fdb)\n  (fftwf_dft_rank_geq2_register 0 #x11bdd #x11bdd #x0 #xe306c0d6 #x621e38d2 #xc1e339ec #xf4f6cc20)\n  (fftwf_dft_nop_register 0 #x10bdd #x10bdd #x0 #xc527c2c6 #xfab4fd30 #x0f5d6b2c #x572ae1aa)\n  (fftwf_codelet_t2fv_20_avx 0 #x10bdd #x10bdd #x0 #xc708f2d3 #x9659f94f #xbd8aa7aa #x0b892dea)\n  (fftwf_dft_bluestein_register 0 #x10bdd #x10bdd #x0 #x21770fdf #x88d8bede #xedd6d3f8 #xf034ac28)\n  (fftwf_dft_r2hc_register 0 #x11bdd #x11bdd #x0 #xcf6484a3 #xeb96624d #x9fb138be #x2d1418ef)\n  (fftwf_rdft_rank0_register 3 #x11bdd #x11bdd #x0 #xce01f425 #xb25c5e42 #x6ff25e8b #x576556a2)\n  (fftwf_dft_buffered_register 0 #x10bdd #x10bdd #x0 #xe696c6ec #xf1746f89 #x5302f428 #xb1105975)\n  (fftwf_dft_generic_register 0 #x11bdd #x11bdd #x0 #x0fe532d1 #x1b0fe2a6 #xe1036c71 #x37ec6e6e)\n  (fftwf_dft_vrank_geq1_register 0 #x11bdd #x11bdd #x0 #xa2f7c7a3 #x11bb3f58 #x8e2bfc2d #x35e8fbd1)\n  (fftwf_dft_nop_register 0 #x11bdd #x11bdd #x0 #xf018e799 #x52a9f6b1 #x88e103d1 #xbc1674aa)\n  (fftwf_codelet_n2fv_16_avx 0 #x10bdd #x10bdd #x0 #xec796509 #xda616af9 #x241273f9 #x4ce72e8f)\n)\n'
+p1
+S'(fftw-3.3.3 fftwl_wisdom #x2fa95cff #x06d4b84e #x4020c7e8 #xcc9b0a2b\n)\n'
+p2
+tp3
+.

pphelper/tests/test_image.py

@@ -0,0 +1,35 @@
+# -*- coding: utf-8 -*-
+
+from pphelper.image import lowpass_filter_image, fft_image
+import numpy as np
+import pyfftw
+import pickle
+
+data_directory = 'pphelper/tests/data/'
+
+
+# def test_lowpass_filter_image():
+#     result = lowpass_filter_image(filename=data_directory + 'tux.png',
+#                                   flatten=True)
+#     result_expected = np.load(
+#         data_directory + 'tux_flattened_lowpass_filtered_sigma_3.npy'
+#     )
+#     assert np.array_equal(result, result_expected)
+#
+#
+# def test_fft_image():
+#     image = np.load(data_directory + 'tux_flattened.npy')
+#
+#     with open(data_directory + 'fftw3-wisdom.pickle', 'rb') as f:
+#         pyfftw.import_wisdom(pickle.load(f))
+#     fft, amplitude, phase = fft_image(image)
+#
+#     fft_expected = np.load(data_directory + 'tux_flattened_fft.npy')
+#     amplitude_expected = np.load(
+#         data_directory + 'tux_flattened_amplitude.npy'
+#     )
+#     phase_expected = np.load(data_directory + 'tux_flattened_phase.npy')
+#
+#     assert np.allclose(fft, fft_expected)
+#     assert np.allclose(amplitude, amplitude_expected)
+#     assert np.allclose(phase, phase_expected)

pphelper/tests/test_racemodel.py

@@ -1,9 +1,5 @@
 # -*- coding: utf-8 -*-
 
-"""
-Unit and (sort-of) integration tests for ``pphelper``.
-"""
-
 from __future__ import division
 import numpy as np
 import pandas as pd

pphelper/version.py

@@ -1 +1 @@
-__version__ = '0.4'
+__version__ = '0.5'

setup.py

@@ -24,8 +24,8 @@
                 'experiments.',
     long_description=open('README.rst').read(),
     install_requires=['sphinxcontrib-napoleon', 'psychopy >= 1.81.03',
-                      'pandas >= 0.14.1', 'matplotlib', 'scipy',
-                      'numpy >= 1.7.2'],
+                      'pyfftw', 'pandas >= 0.14.1', 'matplotlib',
+                      'scipy', 'pillow', 'numpy >= 1.7.2'],
     classifiers=['Intended Audience :: Science/Research',
                  'Programming Language :: Python',
                  'Topic :: Scientific/Engineering :: Bio-Informatics',