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Midnighter/nan_pdist.ipynb

Created July 24, 2014 10:03
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pairwise euclidean distance with missing values
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nan_pdist.ipynb
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"input": [
"import numpy as np\n",
"\n",
"import distance\n",
"\n",
"from numpy.linalg import norm\n",
"from scipy.spatial.distance import pdist"
],
"language": "python",
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{
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"input": [
"def nan_pdist(data):\n",
" m = data.shape[0]\n",
" dm = np.zeros(m * (m - 1) // 2, dtype=float)\n",
" mask = np.isfinite(data)\n",
" vec_mask = np.zeros(data.shape[1], dtype=bool)\n",
" k = 0\n",
" for i in range(m - 1):\n",
" for j in range(i + 1, m):\n",
" vec_mask = np.logical_and(mask[i], mask[j])\n",
" dm[k] = norm(data[i][vec_mask] - data[j][vec_mask])\n",
" k += 1\n",
" return dm"
],
"language": "python",
"metadata": {},
"outputs": [],
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{
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"input": [
"%load_ext cythonmagic"
],
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"input": [
"%%cython -a -lm\n",
"\n",
"cimport cython\n",
"import numpy as np\n",
"cimport numpy as np\n",
"\n",
"from libc.math cimport sqrt\n",
"from numpy cimport (PyArray_DIMS,)\n",
"\n",
"\n",
"np.import_array()\n",
"\n",
"\n",
"@cython.boundscheck(False)\n",
"@cython.wraparound(False)\n",
"cdef inline double nan_euclidean(const double[::1] u, const double[::1] v, const Py_ssize_t n):\n",
" cdef Py_ssize_t c = 0\n",
" cdef double a = 0.0\n",
" cdef double b = 0.0\n",
" cdef double d = 0.0\n",
" cdef double asum = 0.0\n",
" for c in range(n):\n",
" a = u[c]\n",
" if a != a:\n",
" continue\n",
" b = v[c]\n",
" if b != b:\n",
" continue\n",
" d = a - b\n",
" asum += d * d\n",
" return sqrt(asum)\n",
"\n",
"@cython.boundscheck(False)\n",
"@cython.wraparound(False)\n",
"cdef inline double nan_euclidean2(const double[::1] u, const double[::1] v, const Py_ssize_t n):\n",
" cdef Py_ssize_t c = 0\n",
" cdef double d = 0.0\n",
" cdef double a = 0.0\n",
" cdef double b = 0.0\n",
" cdef double asum = 0.0\n",
" for c in range(n):\n",
" a = u[c]\n",
" b = v[c]\n",
" if a == a and b == b:\n",
" d = a - b\n",
" asum += d * d\n",
" return sqrt(asum)\n",
"\n",
"@cython.boundscheck(False)\n",
"@cython.wraparound(False)\n",
"def nan_pdist2(np.ndarray[np.float64_t, ndim=2] data):\n",
" cdef np.npy_intp *dim = PyArray_DIMS(data)\n",
" cdef Py_ssize_t m = dim[0]\n",
" cdef Py_ssize_t n = dim[1]\n",
" cdef Py_ssize_t i = 0\n",
" cdef Py_ssize_t j = 0\n",
" cdef Py_ssize_t k = 0\n",
" cdef double[::1] first\n",
" cdef np.ndarray[np.float64_t, ndim=1] dm = np.zeros(m * (m - 1) // 2, dtype=np.float64)\n",
" for i in range(m - 1):\n",
" first = data[i]\n",
" for j in range(i + 1, m):\n",
" dm[k] = nan_euclidean2(first, data[j], n)\n",
" k += 1\n",
" return dm\n",
"\n",
"@cython.boundscheck(False)\n",
"@cython.wraparound(False)\n",
"def nan_pdist3(np.ndarray[np.float64_t, ndim=2] data):\n",
" cdef np.npy_intp *dim = PyArray_DIMS(data)\n",
" cdef Py_ssize_t m = dim[0]\n",
" cdef Py_ssize_t n = dim[1]\n",
" cdef Py_ssize_t i = 0\n",
" cdef Py_ssize_t j = 0\n",
" cdef Py_ssize_t c = 0\n",
" cdef Py_ssize_t k = 0\n",
" cdef double d = 0.0\n",
" cdef double[:] column\n",
" cdef double[:, :] cont = data\n",
" cdef np.ndarray[np.float64_t, ndim=1] dm = np.zeros(m * (m - 1) // 2, dtype=np.float64)\n",
" for c in range(n):\n",
" column = cont[:, c]\n",
" k = 0\n",
" for i in range(m - 1):\n",
" if column[i] != column[i]:\n",
" k += m - i - 1\n",
" continue\n",
" for j in range(i + 1, m):\n",
" if column[j] == column[j]:\n",
" d = column[i] - column[j]\n",
" dm[k] += d * d\n",
" k += 1\n",
" return np.sqrt(dm)"
],
"language": "python",
"metadata": {},
"outputs": [
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"<p>Generated by Cython 0.20.2 on Thu Jul 24 11:42:21 2014\n",
"<pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line1\")'> 1: </pre>\n",
"<pre id='line1' class='code' style='background-color: #FFFFff'></pre><pre class='line' style='background-color: #FFFF79' onclick='toggleDiv(\"line2\")'> 2: cimport cython</pre>\n",
"<pre id='line2' class='code' style='background-color: #FFFF79'> __pyx_t_1 = <span class='py_c_api'>PyDict_New</span>();<span class='error_goto'> if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;}</span>\n",
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" <span class='pyx_macro_api'>__Pyx_DECREF</span>(__pyx_t_1); __pyx_t_1 = 0;\n",
"</pre><pre class='line' style='background-color: #FFFF8d' onclick='toggleDiv(\"line3\")'> 3: import numpy as np</pre>\n",
"<pre id='line3' class='code' style='background-color: #FFFF8d'> __pyx_t_1 = <span class='pyx_c_api'>__Pyx_Import</span>(__pyx_n_s_numpy, 0, -1);<span class='error_goto'> if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3; __pyx_clineno = __LINE__; goto __pyx_L1_error;}</span>\n",
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" <span class='pyx_macro_api'>__Pyx_DECREF</span>(__pyx_t_1); __pyx_t_1 = 0;\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line4\")'> 4: cimport numpy as np</pre>\n",
"<pre id='line4' class='code' style='background-color: #FFFFff'></pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line5\")'> 5: </pre>\n",
"<pre id='line5' class='code' style='background-color: #FFFFff'></pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line6\")'> 6: from libc.math cimport sqrt</pre>\n",
"<pre id='line6' class='code' style='background-color: #FFFFff'></pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line7\")'> 7: from numpy cimport (PyArray_DIMS,)</pre>\n",
"<pre id='line7' class='code' style='background-color: #FFFFff'></pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line8\")'> 8: </pre>\n",
"<pre id='line8' class='code' style='background-color: #FFFFff'></pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line9\")'> 9: </pre>\n",
"<pre id='line9' class='code' style='background-color: #FFFFff'></pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line10\")'> 10: np.import_array()</pre>\n",
"<pre id='line10' class='code' style='background-color: #FFFFff'> import_array();\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line11\")'> 11: </pre>\n",
"<pre id='line11' class='code' style='background-color: #FFFFff'></pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line12\")'> 12: </pre>\n",
"<pre id='line12' class='code' style='background-color: #FFFFff'></pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line13\")'> 13: @cython.boundscheck(False)</pre>\n",
"<pre id='line13' class='code' style='background-color: #FFFFff'></pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line14\")'> 14: @cython.wraparound(False)</pre>\n",
"<pre id='line14' class='code' style='background-color: #FFFFff'></pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line15\")'> 15: cdef inline double nan_euclidean(const double[::1] u, const double[::1] v, const Py_ssize_t n):</pre>\n",
"<pre id='line15' class='code' style='background-color: #FFFFff'>static CYTHON_INLINE double __pyx_f_46_cython_magic_b9d0f7240e5ef6934fa99b1b891215b5_nan_euclidean(__Pyx_memviewslice const __pyx_v_u, __Pyx_memviewslice const __pyx_v_v, Py_ssize_t const __pyx_v_n) {\n",
" Py_ssize_t __pyx_v_c;\n",
" double __pyx_v_a;\n",
" double __pyx_v_b;\n",
" double __pyx_v_d;\n",
" double __pyx_v_asum;\n",
" double __pyx_r;\n",
" <span class='refnanny'>__Pyx_RefNannyDeclarations</span>\n",
" <span class='refnanny'>__Pyx_RefNannySetupContext</span>(\"nan_euclidean\", 0);\n",
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" return __pyx_r;\n",
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"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line16\")'> 16: cdef Py_ssize_t c = 0</pre>\n",
"<pre id='line16' class='code' style='background-color: #FFFFff'> __pyx_v_c = 0;\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line17\")'> 17: cdef double a = 0.0</pre>\n",
"<pre id='line17' class='code' style='background-color: #FFFFff'> __pyx_v_a = 0.0;\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line18\")'> 18: cdef double b = 0.0</pre>\n",
"<pre id='line18' class='code' style='background-color: #FFFFff'> __pyx_v_b = 0.0;\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line19\")'> 19: cdef double d = 0.0</pre>\n",
"<pre id='line19' class='code' style='background-color: #FFFFff'> __pyx_v_d = 0.0;\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line20\")'> 20: cdef double asum = 0.0</pre>\n",
"<pre id='line20' class='code' style='background-color: #FFFFff'> __pyx_v_asum = 0.0;\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line21\")'> 21: for c in range(n):</pre>\n",
"<pre id='line21' class='code' style='background-color: #FFFFff'> __pyx_t_1 = __pyx_v_n;\n",
" for (__pyx_t_2 = 0; __pyx_t_2 &lt; __pyx_t_1; __pyx_t_2+=1) {\n",
" __pyx_v_c = __pyx_t_2;\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line22\")'> 22: a = u[c]</pre>\n",
"<pre id='line22' class='code' style='background-color: #FFFFff'> __pyx_t_3 = __pyx_v_c;\n",
" __pyx_v_a = (*((double *) ( /* dim=0 */ ((char *) (((double *) __pyx_v_u.data) + __pyx_t_3)) )));\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line23\")'> 23: if a != a:</pre>\n",
"<pre id='line23' class='code' style='background-color: #FFFFff'> __pyx_t_4 = ((__pyx_v_a != __pyx_v_a) != 0);\n",
" if (__pyx_t_4) {\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line24\")'> 24: continue</pre>\n",
"<pre id='line24' class='code' style='background-color: #FFFFff'> goto __pyx_L3_continue;\n",
" }\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line25\")'> 25: b = v[c]</pre>\n",
"<pre id='line25' class='code' style='background-color: #FFFFff'> __pyx_t_5 = __pyx_v_c;\n",
" __pyx_v_b = (*((double *) ( /* dim=0 */ ((char *) (((double *) __pyx_v_v.data) + __pyx_t_5)) )));\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line26\")'> 26: if b != b:</pre>\n",
"<pre id='line26' class='code' style='background-color: #FFFFff'> __pyx_t_4 = ((__pyx_v_b != __pyx_v_b) != 0);\n",
" if (__pyx_t_4) {\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line27\")'> 27: continue</pre>\n",
"<pre id='line27' class='code' style='background-color: #FFFFff'> goto __pyx_L3_continue;\n",
" }\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line28\")'> 28: d = a - b</pre>\n",
"<pre id='line28' class='code' style='background-color: #FFFFff'> __pyx_v_d = (__pyx_v_a - __pyx_v_b);\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line29\")'> 29: asum += d * d</pre>\n",
"<pre id='line29' class='code' style='background-color: #FFFFff'> __pyx_v_asum = (__pyx_v_asum + (__pyx_v_d * __pyx_v_d));\n",
" __pyx_L3_continue:;\n",
" }\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line30\")'> 30: return sqrt(asum)</pre>\n",
"<pre id='line30' class='code' style='background-color: #FFFFff'> __pyx_r = sqrt(__pyx_v_asum);\n",
" goto __pyx_L0;\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line31\")'> 31: </pre>\n",
"<pre id='line31' class='code' style='background-color: #FFFFff'></pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line32\")'> 32: @cython.boundscheck(False)</pre>\n",
"<pre id='line32' class='code' style='background-color: #FFFFff'></pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line33\")'> 33: @cython.wraparound(False)</pre>\n",
"<pre id='line33' class='code' style='background-color: #FFFFff'></pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line34\")'> 34: cdef inline double nan_euclidean2(const double[::1] u, const double[::1] v, const Py_ssize_t n):</pre>\n",
"<pre id='line34' class='code' style='background-color: #FFFFff'>static CYTHON_INLINE double __pyx_f_46_cython_magic_b9d0f7240e5ef6934fa99b1b891215b5_nan_euclidean2(__Pyx_memviewslice const __pyx_v_u, __Pyx_memviewslice const __pyx_v_v, Py_ssize_t const __pyx_v_n) {\n",
" Py_ssize_t __pyx_v_c;\n",
" double __pyx_v_d;\n",
" double __pyx_v_a;\n",
" double __pyx_v_b;\n",
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" return __pyx_r;\n",
"}\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line35\")'> 35: cdef Py_ssize_t c = 0</pre>\n",
"<pre id='line35' class='code' style='background-color: #FFFFff'> __pyx_v_c = 0;\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line36\")'> 36: cdef double d = 0.0</pre>\n",
"<pre id='line36' class='code' style='background-color: #FFFFff'> __pyx_v_d = 0.0;\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line37\")'> 37: cdef double a = 0.0</pre>\n",
"<pre id='line37' class='code' style='background-color: #FFFFff'> __pyx_v_a = 0.0;\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line38\")'> 38: cdef double b = 0.0</pre>\n",
"<pre id='line38' class='code' style='background-color: #FFFFff'> __pyx_v_b = 0.0;\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line39\")'> 39: cdef double asum = 0.0</pre>\n",
"<pre id='line39' class='code' style='background-color: #FFFFff'> __pyx_v_asum = 0.0;\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line40\")'> 40: for c in range(n):</pre>\n",
"<pre id='line40' class='code' style='background-color: #FFFFff'> __pyx_t_1 = __pyx_v_n;\n",
" for (__pyx_t_2 = 0; __pyx_t_2 &lt; __pyx_t_1; __pyx_t_2+=1) {\n",
" __pyx_v_c = __pyx_t_2;\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line41\")'> 41: a = u[c]</pre>\n",
"<pre id='line41' class='code' style='background-color: #FFFFff'> __pyx_t_3 = __pyx_v_c;\n",
" __pyx_v_a = (*((double *) ( /* dim=0 */ ((char *) (((double *) __pyx_v_u.data) + __pyx_t_3)) )));\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line42\")'> 42: b = v[c]</pre>\n",
"<pre id='line42' class='code' style='background-color: #FFFFff'> __pyx_t_4 = __pyx_v_c;\n",
" __pyx_v_b = (*((double *) ( /* dim=0 */ ((char *) (((double *) __pyx_v_v.data) + __pyx_t_4)) )));\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line43\")'> 43: if a == a and b == b:</pre>\n",
"<pre id='line43' class='code' style='background-color: #FFFFff'> __pyx_t_5 = ((__pyx_v_a == __pyx_v_a) != 0);\n",
" if (__pyx_t_5) {\n",
" __pyx_t_6 = ((__pyx_v_b == __pyx_v_b) != 0);\n",
" __pyx_t_7 = __pyx_t_6;\n",
" } else {\n",
" __pyx_t_7 = __pyx_t_5;\n",
" }\n",
" if (__pyx_t_7) {\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line44\")'> 44: d = a - b</pre>\n",
"<pre id='line44' class='code' style='background-color: #FFFFff'> __pyx_v_d = (__pyx_v_a - __pyx_v_b);\n",
"</pre><pre class='line' style='background-color: #FFFFff' onclick='toggleDiv(\"line45\")'> 45: asum += d * d</pre>\n",
"<pre id='line45' class='code' style='background-color: #FFFFff'> __pyx_v_asum = (__pyx_v_asum + (__pyx_v_d * __pyx_v_d));\n",
" goto __pyx_L5;\n",
" }\n",
" __pyx_L5:;\n",
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{
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}
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