Clean up dtw_cort_dist

.gitignore

@@ -5,6 +5,7 @@
 *.so
 *.o
 *.pstats
+*.mod
 
 _build
 build
@@ -24,4 +25,6 @@ ipynb/index.rst
 ipynb/index.html
 
 pyfiles/dtw_cort_dist/V5_cython/*.c
-pyfiles/dtw_cort_dist/V5_cython/*.html
+pyfiles/dtw_cort_dist/V5_cython/*.html
\ No newline at end of file
+**/V*/res_cort.npy
+**/V*/res_dtw.npy
\ No newline at end of file

pyfiles/dtw_cort_dist/V1_numpy_loops/dtw_cort_dist_mat.py → pyfiles/dtw_cort_dist/V0_numpy_loops/dtw_cort_dist_mat.py

@@ -19,8 +19,7 @@ def serie_pair_index_generator(number):
     return (
         (_idx_greater, _idx_lower)
         for _idx_greater in range(number)
-        for _idx_lower in range(number)
-        if _idx_lower < _idx_greater
+        for _idx_lower in range(_idx_greater)
     )
 
 
@@ -39,7 +38,6 @@ def DTWDistance(s1, s2):
     _dtw_mat[0, 0] = abs(s1[0] - s2[0])
 
     #  two special cases : filling first row and columns
-
     for j in range(1, len_s2):
         dist = abs(s1[0] - s2[j])
         _dtw_mat[0, j] = dist + _dtw_mat[0, j - 1]

pyfiles/dtw_cort_dist/V11_numpy_vec/dtw_cort_dist_mat.py → pyfiles/dtw_cort_dist/V1_numpy_vec/dtw_cort_dist_mat.py

@@ -5,7 +5,6 @@ from runpy import run_path
 from pathlib import Path
 
 import numpy as np
-import math
 
 util = run_path(Path(__file__).absolute().parent.parent / "util.py")
 
@@ -20,8 +19,7 @@ def serie_pair_index_generator(number):
     return (
         (_idx_greater, _idx_lower)
         for _idx_greater in range(number)
-        for _idx_lower in range(number)
-        if _idx_lower < _idx_greater
+        for _idx_lower in range(_idx_greater)
     )
 
 
@@ -68,14 +66,12 @@ def cort(s1, s2):
     :rtype: float64
 
     """
-
     slope_1 = s1[1:] - s1[:-1]
     slope_2 = s2[1:] - s2[:-1]
     num = np.sum(slope_1 * slope_2)
     sum_square_x = np.sum(slope_1 * slope_1)
     sum_square_y = np.sum(slope_2 * slope_2)
-
-    return num / (math.sqrt(sum_square_x * sum_square_y))
+    return num / (np.sqrt(sum_square_x * sum_square_y))
 
 
 def compute(series, nb_series):

pyfiles/dtw_cort_dist/V2_c_dtw/dtw_cort_dist_mat.py

@@ -30,8 +30,7 @@ def serie_pair_index_generator(number):
     return (
         (_idx_greater, _idx_lower)
         for _idx_greater in range(number)
-        for _idx_lower in range(number)
-        if _idx_lower < _idx_greater
+        for _idx_lower in range(_idx_greater)
     )
 
 

pyfiles/dtw_cort_dist/V3_c_dtw_cort_vect/dtw_cort_dist_mat.py

@@ -27,8 +27,7 @@ def serie_pair_index_generator(number):
     return (
         (_idx_greater, _idx_lower)
         for _idx_greater in range(number)
-        for _idx_lower in range(number)
-        if _idx_lower < _idx_greater
+        for _idx_lower in range(_idx_greater)
     )
 
 

pyfiles/dtw_cort_dist/V4_c_dtw_c_cort/dtw_cort_dist_mat.py

-#!/usr/bin/python3
+#!/usr/bin/env python3
 
 import numpy as np
 import sysconfig
@@ -25,8 +25,11 @@ def serie_pair_index_generator(number):
     :returns: pairs (lower, greater)
     :rtype: a generator
     """
-    return ((_idx_greater, _idx_lower) for _idx_greater in range(number)
-            for _idx_lower in range(number) if _idx_lower < _idx_greater)
+    return (
+        (_idx_greater, _idx_lower)
+        for _idx_greater in range(number)
+        for _idx_lower in range(_idx_greater)
+    )
 
 
 def cDTW(serie_a, serie_b):
@@ -50,6 +53,7 @@ def cort(serie_a, serie_b):
     ret = dllib.cort(a_ptr, b_ptr, len(serie_a))
     return ret
 
+
 def compute(series, nb_series):
     gen = serie_pair_index_generator(nb_series)
 

pyfiles/dtw_cort_dist/V5_cython/dtw_cort_dist_mat.py

@@ -10,6 +10,7 @@ from dtw_cort import cort, DTWDistance
 
 util = run_path(Path(__file__).absolute().parent.parent / "util.py")
 
+
 def serie_pair_index_generator(number):
     """ generator for pair index (i, j) such that i < j < number
 
@@ -20,8 +21,7 @@ def serie_pair_index_generator(number):
     return (
         (_idx_greater, _idx_lower)
         for _idx_greater in range(number)
-        for _idx_lower in range(number)
-        if _idx_lower < _idx_greater
+        for _idx_lower in range(_idx_greater)
     )
 
 

pyfiles/dtw_cort_dist/V6_pythran_aot/Makefile

 
 all:
-	transonic dtw_cort_dist_mat.py
+	transonic dtw_cort_dist_mat.py -pf "-march=native -O3 -DUSE_XSIMD"
 
 clean:
 	rm -rf __pythran__
\ No newline at end of file

pyfiles/dtw_cort_dist/V6_pythran_aot/dtw_cort_dist_mat.py

@@ -21,8 +21,7 @@ def serie_pair_index_generator(number):
     return (
         (_idx_greater, _idx_lower)
         for _idx_greater in range(number)
-        for _idx_lower in range(number)
-        if _idx_lower < _idx_greater
+        for _idx_lower in range(_idx_greater)
     )
 
 
@@ -62,23 +61,19 @@ def DTWDistance(s1, s2):
 
 
 def cort(s1, s2):
-    """ Computes the cort between serie one and two (assuming they have the same length)
+    """ Computes the cort between series one and two (assuming they have the same length)
 
-    :param s1: the first serie (or any iterable over floats64)
-    :param s2: the second serie (or any iterable over floats64)
+    :param s1: the first series (or any iterable over floats64)
+    :param s2: the second series (or any iterable over floats64)
     :returns: the cort distance
     :rtype: float64
 
     """
-    num = 0.0
-    sum_square_x = 0.0
-    sum_square_y = 0.0
-    for t in range(len(s1) - 1):
-        slope_1 = s1[t + 1] - s1[t]
-        slope_2 = s2[t + 1] - s2[t]
-        num += slope_1 * slope_2
-        sum_square_x += slope_1 * slope_1
-        sum_square_y += slope_2 * slope_2
+    slope_1 = s1[1:] - s1[:-1]
+    slope_2 = s2[1:] - s2[:-1]
+    num = np.sum(slope_1 * slope_2)
+    sum_square_x = np.sum(slope_1 * slope_1)
+    sum_square_y = np.sum(slope_2 * slope_2)
     return num / (np.sqrt(sum_square_x * sum_square_y))
 
 

pyfiles/dtw_cort_dist/V6_pythran/dtw_cort_dist_mat.py → pyfiles/dtw_cort_dist/V6_pythran_jit/dtw_cort_dist_mat.py

@@ -22,8 +22,7 @@ def serie_pair_index_generator(number):
     return (
         (_idx_greater, _idx_lower)
         for _idx_greater in range(number)
-        for _idx_lower in range(number)
-        if _idx_lower < _idx_greater
+        for _idx_lower in range(_idx_greater)
     )
 
 
@@ -63,23 +62,19 @@ def DTWDistance(s1, s2):
 
 
 def cort(s1, s2):
-    """ Computes the cort between serie one and two (assuming they have the same length)
+    """ Computes the cort between series one and two (assuming they have the same length)
 
-    :param s1: the first serie (or any iterable over floats64)
-    :param s2: the second serie (or any iterable over floats64)
+    :param s1: the first series (or any iterable over floats64)
+    :param s2: the second series (or any iterable over floats64)
     :returns: the cort distance
     :rtype: float64
 
     """
-    num = 0.0
-    sum_square_x = 0.0
-    sum_square_y = 0.0
-    for t in range(len(s1) - 1):
-        slope_1 = s1[t + 1] - s1[t]
-        slope_2 = s2[t + 1] - s2[t]
-        num += slope_1 * slope_2
-        sum_square_x += slope_1 * slope_1
-        sum_square_y += slope_2 * slope_2
+    slope_1 = s1[1:] - s1[:-1]
+    slope_2 = s2[1:] - s2[:-1]
+    num = np.sum(slope_1 * slope_2)
+    sum_square_x = np.sum(slope_1 * slope_1)
+    sum_square_y = np.sum(slope_2 * slope_2)
     return num / (np.sqrt(sum_square_x * sum_square_y))
 
 

pyfiles/dtw_cort_dist/V6_pythran_no_transonic/Makefile

 
 all:
-	pythran kernels_pythran.py
+	pythran kernels_pythran.py -march=native -O3 -DUSE_XSIMD
 
 clean:
 	rm -rf *.so
\ No newline at end of file

pyfiles/dtw_cort_dist/V6_pythran_no_transonic/kernels_pythran.py

@@ -6,8 +6,7 @@ def serie_pair_index_generator(number):
     return (
         (_idx_greater, _idx_lower)
         for _idx_greater in range(number)
-        for _idx_lower in range(number)
-        if (_idx_lower < _idx_greater)
+        for _idx_lower in range(_idx_greater)
     )
 
 
@@ -37,17 +36,20 @@ def DTWDistance(s1, s2):
 
 
 def cort(s1, s2):
-    " Computes the cort between serie one and two (assuming they have the same length)\n\n    :param s1: the first serie (or any iterable over floats64)\n    :param s2: the second serie (or any iterable over floats64)\n    :returns: the cort distance\n    :rtype: float64\n\n    "
-    num = 0.0
-    sum_square_x = 0.0
-    sum_square_y = 0.0
-    for t in range((len(s1) - 1)):
-        slope_1 = s1[(t + 1)] - s1[t]
-        slope_2 = s2[(t + 1)] - s2[t]
-        num += slope_1 * slope_2
-        sum_square_x += slope_1 * slope_1
-        sum_square_y += slope_2 * slope_2
-    return num / np.sqrt((sum_square_x * sum_square_y))
+    """ Computes the cort between series one and two (assuming they have the same length)
+
+    :param s1: the first series (or any iterable over floats64)
+    :param s2: the second series (or any iterable over floats64)
+    :returns: the cort distance
+    :rtype: float64
+
+    """
+    slope_1 = s1[1:] - s1[:-1]
+    slope_2 = s2[1:] - s2[:-1]
+    num = np.sum(slope_1 * slope_2)
+    sum_square_x = np.sum(slope_1 * slope_1)
+    sum_square_y = np.sum(slope_2 * slope_2)
+    return num / (np.sqrt(sum_square_x * sum_square_y))
 
 
 # pythran export compute(float64[:, :], int)

pyfiles/dtw_cort_dist/V7_numba/dtw_cort_dist_mat.py

@@ -21,8 +21,7 @@ def serie_pair_index_generator(number):
     return (
         (_idx_greater, _idx_lower)
         for _idx_greater in range(number)
-        for _idx_lower in range(number)
-        if _idx_lower < _idx_greater
+        for _idx_lower in range(_idx_greater)
     )
 
 

pyfiles/dtw_cort_dist/V9_fortran/dtw_cort_dist_mat.py

@@ -20,8 +20,7 @@ def serie_pair_index_generator(number):
     return (
         (_idx_greater, _idx_lower)
         for _idx_greater in range(number)
-        for _idx_lower in range(number)
-        if _idx_lower < _idx_greater
+        for _idx_lower in range(_idx_greater)
     )
 
 
@@ -36,6 +35,7 @@ def DTWDistance(s1, s2):
     dtw_result = dtw_cort.dtwdistance(s1, s2)
     return dtw_result
 
+
 def cort(s1, s2):
     """ Computes the cort between serie one and two (assuming they have the same length)
 

pyfiles/dtw_cort_dist/util.py

@@ -17,8 +17,7 @@ def serie_pair_index_generator(number):
     return (
         (_idx_greater, _idx_lower)
         for _idx_greater in range(number)
-        for _idx_lower in range(number)
-        if _idx_lower < _idx_greater
+        for _idx_lower in range(_idx_greater)
     )
 
 

requirements.txt

@@ -17,6 +17,7 @@ cffi
 cython
 numba
 pythran
+xsimd
 transonic
 # parallel
 mpi4py