Rewrite conv_func classes to use ABC base for truncation.

Rewrite tests to be neater, easier to read.

Add py34 to testing regime.

Author: timstaley

.travis.yml

@@ -3,6 +3,8 @@ matrix:
   include:
     - python: "2.7"
       env: TOXENV=py27
+    - python: "3.4"
+      env: TOXENV=py34
     - python: "2.7"
       env: TOXENV=docs
 
@@ -19,4 +21,4 @@ notifications:
     on_success: never
     on_failure: always
 
-sudo: false
+sudo: false

docs/Makefile

@@ -2,7 +2,7 @@
 #
 
 # You can set these variables from the command line.
-SPHINXOPTS    =
+SPHINXOPTS    = -Wv
 SPHINXBUILD   = sphinx-build
 PAPER         =
 BUILDDIR      = build

docs/source/conf.py

@@ -68,7 +68,7 @@
 todo_include_todos = False
 
 
-autoclass_content = 'both'
+autoclass_content = 'class'
 # napoleon_use_ivar = True
 
 # Warn when references cannot be resolved:

docs/standalone_notebooks/convolutional_kernel_funcs.ipynb

@@ -19,7 +19,7 @@
     "import matplotlib.pyplot as plt\n",
     "import matplotlib.image as mpimg\n",
     "import numpy as np\n",
-    "%matplotlib inline\n",
+    "%matplotlib notebook\n",
     "# Plot image pixels in cartesian ordering (i.e. y-positive == upwards):\n",
     "plt.rcParams['image.origin'] = 'lower'\n",
     "# Make plots bigger\n",
@@ -41,12 +41,25 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true
+    "collapsed": false
    },
    "outputs": [],
    "source": [
     "triangle3 = conv_funcs.Triangle(half_base_width=3.0)\n",
-    "pillbox = conv_funcs.Pillbox(half_base_width=2.5)"
+    "pillbox = conv_funcs.Pillbox(half_base_width=2.5)\n",
+    "sinc = conv_funcs.Sinc(3)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "plot_radius = 10.\n",
+    "x=np.linspace(-plot_radius,plot_radius,101)"
    ]
   },
   {
@@ -57,7 +70,7 @@
    },
    "outputs": [],
    "source": [
-    "x=np.linspace(-4.,4.,81)"
+    "sinc([-5.])"
    ]
   },
   {
@@ -68,29 +81,30 @@
    },
    "outputs": [],
    "source": [
+    "# plt.plot(x, pillbox(x), color='r')\n",
     "plt.plot(x, triangle3(x), color='g')\n",
-    "plt.plot(x, pillbox(x), color='r')\n",
-    "plt.ylim(0,1.1)"
+    "plt.plot(x, sinc(x), color='b')\n",
+    "plt.ylim(-0.5,1.1)"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 2",
    "language": "python",
-   "name": "python3"
+   "name": "python2"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 3
+    "version": 2
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.4.3"
+   "pygments_lexer": "ipython2",
+   "version": "2.7.6"
   }
  },
  "nbformat": 4,

setup.py

@@ -9,6 +9,7 @@
     'click',
     'pandas',
     'pytest',
+    'six',
     'scipy',
 ]
 

src/fastimgproto/gridder/conv_funcs.py

@@ -10,10 +10,41 @@
 """
 from attr import attrs, attrib
 import numpy as np
+from six import add_metaclass
+from abc import ABCMeta, abstractmethod
 
 
-@attrs
-class Triangle(object):
+@add_metaclass(ABCMeta)
+class ConvFuncBase(object):
+    """
+    Implements truncation (via __call__), numpy array reshaping.
+
+    Always returns 0 outside truncation radius, i.e.::
+
+        if np.fabs(x) > trunc:
+            conv_func(x)==0 # True
+
+    Args:
+        trunc: truncation radius.
+    """
+
+    def __init__(self, trunc):
+        self.trunc = trunc
+
+    @abstractmethod
+    def f(self, radius):
+        """The convolution function to be evaluated and truncated"""
+        pass
+
+    def __call__(self, radius_in_pix):
+        radius_in_pix = np.atleast_1d(radius_in_pix)
+        output = np.zeros_like(radius_in_pix)
+        inside_trunc_radius = np.fabs(radius_in_pix) < self.trunc
+        output[inside_trunc_radius] = self.f(radius_in_pix[inside_trunc_radius])
+        return output
+
+
+class Triangle(ConvFuncBase):
     """
     Linearly declines from 1.0 at origin to 0.0 at **half_base_width**, zero thereafter.
     "
@@ -28,17 +59,19 @@ class Triangle(object):
         half_base_width (float): Half-base width of the triangle.
 
     """
-    half_base_width = attrib()
 
-    def __call__(self, radius_in_pix):
+    def __init__(self, half_base_width):
+        self.half_base_width = half_base_width
+        super(Triangle, self).__init__(half_base_width)
+
+    def f(self, radius_in_pix):
         return np.maximum(
             1.0 - np.fabs(radius_in_pix) / self.half_base_width,
             np.zeros_like(radius_in_pix)
         )
 
 
-@attrs
-class Pillbox(object):
+class Pillbox(ConvFuncBase):
     """
     Valued 1.0 from origin to **half_base_width**, zero thereafter.
 
@@ -53,7 +86,44 @@ class Pillbox(object):
     Attributes:
         half_base_width (float): Half-base width pillbox.
     """
-    half_base_width = attrib()
 
-    def __call__(self, radius_in_pix):
+    def __init__(self, half_base_width):
+        self.half_base_width = half_base_width
+        super(Pillbox, self).__init__(half_base_width)
+
+    def f(self, radius_in_pix):
         return np.where(np.fabs(radius_in_pix) < self.half_base_width, 1.0, 0.0)
+
+
+class Sinc(ConvFuncBase):
+    """
+    Sinc function, truncated beyond **trunc** pixels from centre.
+
+
+    Attributes:
+        trunc (float): Truncation radius
+    """
+    trunc = attrib(default=3.0)
+
+    def __init__(self, trunc):
+        super(Sinc, self).__init__(trunc)
+
+    def f(self, radius_in_pix):
+        return np.sinc(radius_in_pix)
+
+
+class Sinc(ConvFuncBase):
+    """
+    Sinc function, truncated beyond **trunc** pixels from centre.
+
+
+    Attributes:
+        trunc (float): Truncation radius
+    """
+    trunc = attrib(default=3.0)
+
+    def __init__(self, trunc):
+        super(Sinc, self).__init__(trunc)
+
+    def f(self, radius_in_pix):
+        return np.sinc(radius_in_pix)

tests/test_gridder/test_conv_funcs.py

@@ -2,32 +2,59 @@
 import numpy as np
 
 
-def test_triangle_func():
-    triangle2 = conv_funcs.Triangle(half_base_width=2.0)
-
-    # Test known simple inputs
-    assert triangle2(0.0) == 1.0
-    assert triangle2(1.0) == 0.5
-    assert triangle2(2.0) == 0.0
-    assert triangle2(2.000001) == 0.0
-    assert triangle2(100) == 0.0
-    assert triangle2(-0.1) == triangle2(0.1)
+def check_function_results_close(func, input_output_pairs,
+                                 symmetric=True,
+                                 eps=1e-15):
+    # test with scalar inputs
+    for pair in input_output_pairs:
+        assert np.fabs(func(pair[0]) - pair[1]) < eps
 
     # test with array input
-    input = np.array([-2., 0.0, 0.5, 1.0, 2.0, 3.0])
-    output = np.array([0, 1.0, 0.75, 0.5, 0.0, 0.0])
-    assert (triangle2(input) == output).all()
+    inputs = input_output_pairs[:, 0]
+    outputs = input_output_pairs[:, 1]
+    assert (np.fabs(func(inputs) - outputs) < eps).all()
+    if symmetric:
+        inputs *= -1.0
+        assert (np.fabs(func(inputs) - outputs) < eps).all()
 
 
-def test_tophat_funct():
-    tophat3 = conv_funcs.Pillbox(half_base_width=3.0)
+def test_triangle_func():
+    triangle2 = conv_funcs.Triangle(half_base_width=2.0)
 
-    input = np.array([-4.2, -2.5, 0.0, 1.5, 2.999, 3.0, 3.1])
-    output = np.array([0.0, 1.0, 1.0, 1., 1., 0.0, 0.0])
+    io_pairs = np.array([
+        [0.0, 1.0],
+        [1.0, 0.5],
+        [2.0, 0.0],
+        [2.000001, 0.0],
+        [100, 0.0],
+        [0.1, 0.95],
+        [0.5, 0.75],
+    ])
 
-    # test with array input
-    assert (tophat3(input) == output).all()
+    check_function_results_close(triangle2, io_pairs)
 
-    # test with scalar input
-    for idx, val in enumerate(input):
-        assert tophat3(val) == output[idx]
+
+def test_tophat_func():
+    tophat3 = conv_funcs.Pillbox(half_base_width=3.0)
+    io_pairs = np.array([
+        [0.0, 1.0],
+        [2.5, 1.0],
+        [2.999, 1.0],
+        [3.0, 0.0],
+        [4.2,0.],
+    ])
+    check_function_results_close(tophat3, io_pairs)
+
+
+def test_sinc():
+    sinc = conv_funcs.Sinc(trunc=3.0)
+    io_pairs = np.array([
+        [0.0, 1.0],
+        [1.0, 0.0],
+        [0.5, 1. / (0.5 * np.pi)],
+        [1.5, -1. / (1.5*np.pi)],
+        [2.0, 0.0],
+        [2.5, 1. / (2.5*np.pi)],
+        [3.5, 0.], # Truncated
+    ])
+    check_function_results_close(sinc, io_pairs)

tests/test_sourcefind/test_detection.py

@@ -36,8 +36,8 @@ def test_basic_source_detection():
                          rms_est=rms)
     assert len(sf.islands) == 1
     src = sf.islands[0]
-    print bright_src
-    print src
+    # print(bright_src)
+    # print(src)
     assert np.abs(src.peak_x_idx - bright_src.x_mean) <0.5
     assert np.abs(src.peak_y_idx - bright_src.y_mean) <0.5
     assert np.abs(src.xbar - bright_src.x_mean) <0.1

tox.ini

@@ -1,13 +1,13 @@
 [tox]
-envlist = py27, docs
+envlist = py27, py34, docs
 
 [testenv]
 deps= pytest
 commands=./runtests.py -sv
 
 [testenv:docs]
 changedir=docs
-deps=-rrequirements/docs.txt
+deps=-rdocs/requirements.txt
 #NBSphinx requires pandoc
 whitelist_externals =
     pandoc