Merge pull request #1 from tomography/master

resync

.gitignore

@@ -33,6 +33,7 @@ var/
 # Installer logs
 pip-log.txt
 pip-delete-this-directory.txt
+commit_hash.txt
 
 # Unit test / coverage reports
 htmlcov/

.travis.yml

@@ -10,6 +10,11 @@ os:
 
 sudo: false
 
+before_script:
+  - "export DISPLAY=:99.0"
+  - "sh -e /etc/init.d/xvfb start"
+  - sleep 3 # give xvfb some time to start
+
 before_install:
   - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
       wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;

docs/demos/Shepp.ipynb

@@ -0,0 +1,131 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Simple Phantom Construction Demo"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Import tomography/xdesign."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "from xdesign import *"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Create various `Features` with geometries. Assign attenuation `values` to each of the `Features`. Plot the `Phantom`."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "head = Feature(Circle(Point(0.5, 0.5), radius=0.5))\n",
+    "head.mass_atten = 1\n",
+    "eyeL = Feature(Circle(Point(0.3, 0.5), radius=0.1))\n",
+    "eyeL.mass_atten = 1\n",
+    "eyeR = Feature(Circle(Point(0.7, 0.5), radius=0.1))\n",
+    "eyeR.mass_atten = 1\n",
+    "mouth = Feature(Triangle(Point(0.2, 0.7), Point(0.5, 0.8), Point(0.8, 0.7)))\n",
+    "mouth.mass_atten = -1\n",
+    "\n",
+    "Shepp = Phantom()\n",
+    "Shepp.append(head)\n",
+    "Shepp.append(eyeL)\n",
+    "Shepp.append(eyeR)\n",
+    "Shepp.append(mouth)\n",
+    "\n",
+    "sidebyside(Shepp, size=100, labels=True)\n",
+    "plt.savefig('Shepp_sidebyside.png', dpi=600,\n",
+    "        orientation='landscape', papertype=None, format=None,\n",
+    "        transparent=True, bbox_inches='tight', pad_inches=0.0,\n",
+    "        frameon=False)\n",
+    "plt.show()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Simulate data acquisition for parallel beam around 180 degrees."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "sx, sy = 100, 100\n",
+    "step = 1. / sy\n",
+    "prb = Probe(Point(step / 2., -10), Point(step / 2., 10), step)\n",
+    "theta = np.pi / sx\n",
+    "sino = np.zeros(sx * sy)\n",
+    "a = 0\n",
+    "for m in range(sx):\n",
+    "    for n in range(sy):\n",
+    "        update_progress((m*sy + n)/(sx*sy))\n",
+    "        sino[a] = prb.measure(Shepp)\n",
+    "        a += 1\n",
+    "        prb.translate(step)\n",
+    "    prb.translate(-1)\n",
+    "    prb.rotate(theta, Point(0.5, 0.5))\n",
+    "update_progress(1)\n",
+    "\n",
+    "plt.figure(figsize=(8, 8))\n",
+    "plt.imshow(np.reshape(sino, (sx, sy)), cmap='inferno', interpolation='nearest')\n",
+    "plt.savefig('Shepp_sinogram.png', dpi=600,\n",
+    "        orientation='landscape', papertype=None, format=None,\n",
+    "        transparent=True, bbox_inches='tight', pad_inches=0.0,\n",
+    "        frameon=False)\n",
+    "plt.show()"
+   ]
+  }
+ ],
+ "metadata": {
+  "anaconda-cloud": {},
+  "kernelspec": {
+   "display_name": "Python [default]",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.5.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 1
+}

setup.py

@@ -47,10 +47,17 @@
 # #########################################################################
 
 import setuptools
+from version_hashtag import append_dev_info
+
+version_info = (0, 1, 0)
+version = '.'.join([str(x) for x in version_info])
+version = append_dev_info(version)
+with open('VERSION', 'w') as f:
+    f.write(version)
 
 setuptools.setup(
     name='xdesign',
-    version=open('VERSION').read().strip(),
+    version=version,
     author='Doga Gursoy',
     description='Benchmarking and optimization tools for tomography.',
     packages=setuptools.find_packages(exclude=['docs']),
@@ -72,6 +79,6 @@
         'Topic :: Software Development :: Libraries',
         'Intended Audience :: Science/Research',
         'Intended Audience :: Education',
-        'Intended Audience :: Developers',
-    ],
+        'Intended Audience :: Developers'
+    ]
 )

tests/test_geometry.py

@@ -52,7 +52,7 @@
 from xdesign.geometry import *
 from xdesign.geometry import beamcirc
 from xdesign.acquisition import *
-from numpy.testing import assert_allclose, assert_raises
+from numpy.testing import assert_allclose, assert_raises, assert_equal
 import numpy as np
 
 
@@ -174,6 +174,43 @@ def test_Circle_area():
     assert_allclose(circle.area, 3.14159265359, rtol=1e-6)
 
 
+def test_Mesh_area():
+    p5 = Point(0, 0)
+    p1 = Point(1, 1)
+    p4 = Point(1, -1)
+    p3 = Point(-1, -1)
+    p2 = Point(-1, 1)
+    m = Mesh()
+    assert_equal(m.area, 0)
+    m.append(Triangle(p5, p1, p2))
+    m.append(Triangle(p5, p2, p3))
+    m.append(Triangle(p5, p3, p4))
+    m.append(Triangle(p5, p4, p1))
+    assert_equal(m.area, 4)
+
+
+def test_Mesh_center():
+    p5 = Point(0, 0)
+    p1 = Point(1, 1)
+    p4 = Point(1, -1)
+    p3 = Point(-1, -1)
+    p2 = Point(-1, 1)
+    m = Mesh()
+    assert_equal(m.center, Point(0, 0))
+
+    m.append(Triangle(p5, p1, p2))
+    m.append(Triangle(p5, p2, p3))
+    m.append(Triangle(p5, p3, p4))
+    m.append(Triangle(p5, p4, p1))
+    assert_equal(m.center, Point(0, 0))
+
+    m.pop()
+    m.pop()
+    m.pop()
+    m.pop()
+    assert_equal(m.center, Point(0, 0))
+
+
 if __name__ == '__main__':
     import nose
     nose.runmodule(exit=False)

tests/test_material.py

@@ -53,6 +53,7 @@
 import numpy as np
 import scipy
 import matplotlib.pyplot as plt
+import warnings
 
 __author__ = "Daniel Ching"
 __copyright__ = "Copyright (c) 2016, UChicago Argonne, LLC."
@@ -72,11 +73,11 @@ def _plot_both(ref, target):
 def test_HyperbolicCocentric():
     p0 = Phantom()
     p0.load('tests/HyperbolicConcentric.txt')
-    ref = p0.discrete(200, uniform=False)
+    ref = discrete_phantom(p0, 200, uniform=False)
 
     np.random.seed(0)
     p = HyperbolicConcentric()
-    target = p.discrete(200, uniform=False)
+    target = discrete_phantom(p, 200, uniform=False)
 
     # _plot_both(ref, target)
     assert_equal(target, ref,
@@ -87,35 +88,37 @@ def test_DynamicRange():
     for i in range(0, 2):
         p0 = Phantom()
         p0.load('tests/DynamicRange'+str(i)+'.txt')
-        ref = p0.discrete(100)
+        ref = discrete_phantom(p0, 100)
 
         np.random.seed(0)
         p = DynamicRange(jitter=i)
-        target = p.discrete(100)
+        target = discrete_phantom(p, 100)
         # _plot_both(ref, target)
         assert_equal(target, ref, "Default DynamicRange" + str(i) +
                                   " phantom has changed.")
 
 
 def test_Soil():
+    warnings.filterwarnings("ignore", "Reached*", RuntimeWarning)
     p0 = Phantom()
     p0.load('tests/Soil.txt')
-    ref = p0.discrete(100)
+    ref = discrete_phantom(p0, 100)
 
     np.random.seed(0)
     p = Soil()
-    target = p.discrete(100)
+    target = discrete_phantom(p, 100)
     # _plot_both(ref, target)
     assert_equal(target, ref, "Default Soil phantom has changed.")
 
 
 def test_Foam():
+    warnings.filterwarnings("ignore", "Reached*", RuntimeWarning)
     p0 = Phantom()
     p0.load('tests/Foam.txt')
-    ref = p0.discrete(100)
+    ref = discrete_phantom(p0, 100)
 
     np.random.seed(0)
     p = Foam()
-    target = p.discrete(100)
+    target = discrete_phantom(p, 100)
     # _plot_both(ref, target)
     assert_equal(target, ref, "Default Foam phantom has changed.")