sci-libs/scikits_image: Version Bump

Package-Manager: portage-2.2.23
Signed-off-by: Justin Lecher <jlec@gentoo.org>

4 files changed, 219 insertions, 0 deletions

diff --git a/sci-libs/scikits_image/Manifest b/sci-libs/scikits_image/Manifest
index 129ffec7301..2f1b123442a 100644
--- a/sci-libs/scikits_image/Manifest
+++ b/sci-libs/scikits_image/Manifest
@@ -1,3 +1,4 @@
 DIST scikit-image-0.10.0.tar.gz 9084596 SHA256 83995570f11654b47d0a0d50ae8b4d11a0de97a44ae195a4c04ba4f10b9dd7f8 SHA512 be45359fe99499e904b0b0e75870cd301947ca1edc7711ce982d107b1e56c0d15cfd59fe8dcc9eff1bca5b1e4bac5ae23e7adeda028590ea1230db76914b0ab8 WHIRLPOOL adeed1d7f6f7b5a5b01c78672226425d481e9dbb69c36f5927274d91856745f472abd8d055c3ad1f880c348d92d5a1bbca9e4253983e7d3aa01ab2f2dfbe29f1
 DIST scikit-image-0.10.1.tar.gz 16740044 SHA256 83a1afcc16df75ff27237f84841a95c8f65c4e19ffd64849faa540aab48a5ab7 SHA512 1fb7c96646775c1015267359ed23916abcc21caa3dd3f31e1d78aedb3994ae56d2cb5b79221e90e2b1997a23dc34679fc6863387bd6bdc9d0e006416c402473a WHIRLPOOL ddd38401dc29535610d7d9a8014aa36b955e1ba0ae6db6ada4ce2151ca323b25134b3cc5635a9e3f06c86b414311c52dab8dd477665fd6ef266087943da4c6de
+DIST scikit-image-0.11.3.tar.gz 18589296 SHA256 768e568f3299966c294b7eb8cd114fc648f7bfaef422ee9cc750dd8d9d09e44b SHA512 595acb66581ed3ca9679b7f031876e1974000a82ec0eccd14bfd283f829aa3db0fcca10166f4260138698f82b3a772fea83d77761a64fab45bbc35418ade7108 WHIRLPOOL 43b52943ac3ff40f58863fdfbf588b5f17d6103e2cf2ec09863006da2a288412cc550d47f8c97027904827ccdd5e12a87ec94620d5788273c364276c2f614c6c
 DIST scikit-image-0.9.3.tar.gz 7829788 SHA256 2c29c65aacdfc056efd0a3b713b5dde666356ffb39e5e2bad3e0d6dbb62524b3 SHA512 4c34a374c19a54da409a99e610b5de7525a0d738f373f5e9ac172c4f2fb520190b61fb30b56db3efd4f62f56e5bbdea6ed20620bbbb41171aca56d5fc5ede900 WHIRLPOOL 1f7509a857bfb7cc1f7cd3d2251b90ac128f8acf14dc5174be3b0337a1bfdec6326fe6b46ae674bdd50ecf23e82fa8f56f53322d887a0d4b52c0015b1dd189b5
diff --git a/sci-libs/scikits_image/files/scikits_image-0.11.3-adapthist-backport.patch b/sci-libs/scikits_image/files/scikits_image-0.11.3-adapthist-backport.patch
new file mode 100644
index 00000000000..0bd96916bfc
--- /dev/null
+++ b/sci-libs/scikits_image/files/scikits_image-0.11.3-adapthist-backport.patch
@@ -0,0 +1,82 @@
+From 41159f3fd24e7653c556ddbf6ba93ad2aa8b541f Mon Sep 17 00:00:00 2001
+From: Steven Silvester <steven.silvester@ieee.org>
+Date: Mon, 19 Oct 2015 18:07:32 -0500
+Subject: [PATCH] Fix adapthist mask logic
+
+Use minlength in bincount
+
+Fix mask logic
+---
+ skimage/exposure/_adapthist.py          |  8 +++++---
+ skimage/exposure/tests/test_exposure.py | 14 +++++++-------
+ 2 files changed, 12 insertions(+), 10 deletions(-)
+
+diff --git a/skimage/exposure/_adapthist.py b/skimage/exposure/_adapthist.py
+index 343f71b..757daff 100644
+--- a/skimage/exposure/_adapthist.py
++++ b/skimage/exposure/_adapthist.py
+@@ -247,12 +247,14 @@ def clip_histogram(hist, clip_limit):
+     while n_excess > 0:  # Redistribute remaining excess
+         index = 0
+         while n_excess > 0 and index < hist.size:
++            under_mask = hist < 0
+             step_size = int(hist[hist < clip_limit].size / n_excess)
+             step_size = max(step_size, 1)
+             indices = np.arange(index, hist.size, step_size)
+-            under = hist[indices] < clip_limit
+-            hist[under] += 1
+-            n_excess -= hist[under].size
++            under_mask[indices] = True
++            under_mask = (under_mask) & (hist < clip_limit)
++            hist[under_mask] += 1
++            n_excess -= under_mask.sum()
+             index += 1
+ 
+     return hist
+diff --git a/skimage/exposure/tests/test_exposure.py b/skimage/exposure/tests/test_exposure.py
+index 8fb6d62..1b9c778 100644
+--- a/skimage/exposure/tests/test_exposure.py
++++ b/skimage/exposure/tests/test_exposure.py
+@@ -199,9 +199,9 @@ def test_adapthist_scalar():
+     full_scale = skimage.exposure.rescale_intensity(skimage.img_as_float(img))
+ 
+     assert_almost_equal = np.testing.assert_almost_equal
+-    assert_almost_equal(peak_snr(full_scale, adapted), 101.2295, 3)
++    assert_almost_equal(peak_snr(full_scale, adapted), 102.066, 3)
+     assert_almost_equal(norm_brightness_err(full_scale, adapted),
+-                        0.041, 3)
++                        0.038, 3)
+     return img, adapted
+ 
+ 
+@@ -217,8 +217,8 @@ def test_adapthist_grayscale():
+                                               nbins=128)
+     assert_almost_equal = np.testing.assert_almost_equal
+     assert img.shape == adapted.shape
+-    assert_almost_equal(peak_snr(img, adapted), 97.6876, 3)
+-    assert_almost_equal(norm_brightness_err(img, adapted), 0.0591, 3)
++    assert_almost_equal(peak_snr(img, adapted), 102.078, 3)
++    assert_almost_equal(norm_brightness_err(img, adapted), 0.0529, 3)
+     return data, adapted
+ 
+ 
+@@ -238,7 +238,7 @@ def test_adapthist_color():
+     assert adapted.max() == 1.0
+     assert img.shape == adapted.shape
+     full_scale = skimage.exposure.rescale_intensity(img)
+-    assert_almost_equal(peak_snr(full_scale, adapted), 109.6, 1)
++    assert_almost_equal(peak_snr(full_scale, adapted), 109.393, 1)
+     assert_almost_equal(norm_brightness_err(full_scale, adapted), 0.02, 2)
+     return data, adapted
+ 
+@@ -256,8 +256,8 @@ def test_adapthist_alpha():
+     full_scale = skimage.exposure.rescale_intensity(img)
+     assert img.shape == adapted.shape
+     assert_almost_equal = np.testing.assert_almost_equal
+-    assert_almost_equal(peak_snr(full_scale, adapted), 109.60, 2)
+-    assert_almost_equal(norm_brightness_err(full_scale, adapted), 0.0235, 3)
++    assert_almost_equal(peak_snr(full_scale, adapted), 109.393, 2)
++    assert_almost_equal(norm_brightness_err(full_scale, adapted), 0.0248, 3)
+ 
+ 
+ def peak_snr(img1, img2):
diff --git a/sci-libs/scikits_image/files/scikits_image-0.11.3-adapthist-backport.patch1 b/sci-libs/scikits_image/files/scikits_image-0.11.3-adapthist-backport.patch1
new file mode 100644
index 00000000000..9d8036c2a1d
--- /dev/null
+++ b/sci-libs/scikits_image/files/scikits_image-0.11.3-adapthist-backport.patch1
@@ -0,0 +1,73 @@
+ skimage/exposure/_adapthist.py          |  8 +++++---
+ skimage/exposure/tests/test_exposure.py | 14 +++++++-------
+ 2 files changed, 12 insertions(+), 10 deletions(-)
+
+diff --git a/skimage/exposure/_adapthist.py b/skimage/exposure/_adapthist.py
+index b71916f..e878bfb 100644
+--- a/skimage/exposure/_adapthist.py
++++ b/skimage/exposure/_adapthist.py
+@@ -255,12 +255,14 @@ def clip_histogram(hist, clip_limit):
+     while n_excess > 0:  # Redistribute remaining excess
+         index = 0
+         while n_excess > 0 and index < hist.size:
++            under_mask = hist < 0
+             step_size = int(hist[hist < clip_limit].size / n_excess)
+             step_size = max(step_size, 1)
+             indices = np.arange(index, hist.size, step_size)
+-            under = hist[indices] < clip_limit
+-            hist[under] += 1
+-            n_excess -= hist[under].size
++            under_mask[indices] = True
++            under_mask = (under_mask) & (hist < clip_limit)
++            hist[under_mask] += 1
++            n_excess -= under_mask.sum()
+             index += 1
+ 
+     return hist
+diff --git a/skimage/exposure/tests/test_exposure.py b/skimage/exposure/tests/test_exposure.py
+index 265ce24..83bb551 100644
+--- a/skimage/exposure/tests/test_exposure.py
++++ b/skimage/exposure/tests/test_exposure.py
+@@ -199,9 +199,9 @@ def test_adapthist_scalar():
+     full_scale = skimage.exposure.rescale_intensity(skimage.img_as_float(img))
+ 
+     assert_almost_equal = np.testing.assert_almost_equal
+-    assert_almost_equal(peak_snr(full_scale, adapted), 101.2295, 3)
++    assert_almost_equal(peak_snr(full_scale, adapted), 102.066, 3)
+     assert_almost_equal(norm_brightness_err(full_scale, adapted),
+-                        0.041, 3)
++                        0.038, 3)
+     return img, adapted
+ 
+ 
+@@ -216,8 +216,8 @@ def test_adapthist_grayscale():
+                                               nbins=128)
+     assert_almost_equal = np.testing.assert_almost_equal
+     assert img.shape == adapted.shape
+-    assert_almost_equal(peak_snr(img, adapted), 97.6876, 3)
+-    assert_almost_equal(norm_brightness_err(img, adapted), 0.0591, 3)
++    assert_almost_equal(peak_snr(img, adapted), 102.078, 3)
++    assert_almost_equal(norm_brightness_err(img, adapted), 0.0529, 3)
+     return data, adapted
+ 
+ 
+@@ -237,7 +237,7 @@ def test_adapthist_color():
+     assert adapted.max() == 1.0
+     assert img.shape == adapted.shape
+     full_scale = skimage.exposure.rescale_intensity(img)
+-    assert_almost_equal(peak_snr(full_scale, adapted), 109.6, 1)
++    assert_almost_equal(peak_snr(full_scale, adapted), 109.393, 1)
+     assert_almost_equal(norm_brightness_err(full_scale, adapted), 0.02, 2)
+     return data, adapted
+ 
+@@ -255,8 +255,8 @@ def test_adapthist_alpha():
+     full_scale = skimage.exposure.rescale_intensity(img)
+     assert img.shape == adapted.shape
+     assert_almost_equal = np.testing.assert_almost_equal
+-    assert_almost_equal(peak_snr(full_scale, adapted), 109.60, 2)
+-    assert_almost_equal(norm_brightness_err(full_scale, adapted), 0.0235, 3)
++    assert_almost_equal(peak_snr(full_scale, adapted), 109.393, 2)
++    assert_almost_equal(norm_brightness_err(full_scale, adapted), 0.0248, 3)
+ 
+ 
+ def peak_snr(img1, img2):
diff --git a/sci-libs/scikits_image/scikits_image-0.11.3.ebuild b/sci-libs/scikits_image/scikits_image-0.11.3.ebuild
new file mode 100644
index 00000000000..02bc1df4899
--- /dev/null
+++ b/sci-libs/scikits_image/scikits_image-0.11.3.ebuild
@@ -0,0 +1,63 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 python3_{3,4} )
+
+inherit distutils-r1 eutils virtualx
+
+MYPN="${PN/scikits_/scikit-}"
+MYP="${MYPN}-${PV}"
+
+DESCRIPTION="Image processing routines for SciPy"
+HOMEPAGE="http://scikit-image.org/"
+SRC_URI="mirror://pypi/${PN:0:1}/${MYPN}/${MYP}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc freeimage gtk pyamg qt4 test"
+
+RDEPEND="
+	>=dev-python/matplotlib-1.1.0[${PYTHON_USEDEP}]
+	>=dev-python/networkx-1.8[${PYTHON_USEDEP}]
+	>=dev-python/numpy-1.6.1[${PYTHON_USEDEP}]
+	>=dev-python/pillow-1.7.8[${PYTHON_USEDEP}]
+	>=dev-python/six-1.3[${PYTHON_USEDEP}]
+	>=sci-libs/scipy-0.9[sparse,${PYTHON_USEDEP}]
+	freeimage? ( media-libs/freeimage )
+	gtk? ( dev-python/pygtk[$(python_gen_usedep 'python2*')] )
+	pyamg? ( dev-python/pyamg[$(python_gen_usedep 'python2*')] )
+	qt4? ( dev-python/PyQt4[${PYTHON_USEDEP}] )"
+DEPEND="${RDEPEND}
+	>=dev-python/cython-0.21[${PYTHON_USEDEP}]
+	dev-python/setuptools[${PYTHON_USEDEP}]
+	test? (
+		dev-python/nose[${PYTHON_USEDEP}]
+		)"
+
+S="${WORKDIR}/${MYP}"
+
+DOCS=( CONTRIBUTORS.txt CONTRIBUTING.txt DEPENDS.txt RELEASE.txt TASKS.txt TODO.txt )
+
+PATCHES=(
+	"${FILESDIR}"/${P}-adapthist-backport.patch
+)
+
+python_test() {
+	distutils_install_for_testing
+	mkdir for_test && cd for_test || die
+	echo "backend : Agg" > matplotlibrc || die
+	echo "backend.qt4 : PyQt4" >> matplotlibrc || die
+	#echo "backend.qt4 : PySide" >> matplotlibrc || die
+	VIRTUALX_COMMAND=nosetests
+	MPLCONFIGDIR=. virtualmake --exe -v skimage || die
+}
+
+pkg_postinst() {
+	optfeature "FITS io capability" dev-python/astropy
+	#optfeature "io plugin providing a wide variety of formats, including specialized formats using in medical imaging." dev-python/simpleitk
+	#optfeature "io plugin providing most standard formats" dev-python/imread
+}