Related
I have two ordered lists of consecutive integers m=0, 1, ... M and n=0, 1, 2, ... N. Each value of m has a probability pm, and each value of n has a probability pn. I am trying to find the ordered list of unique values r=n/m and their probabilities pr. I am aware that r is infinite if n=0 and can even be undefined if m=n=0.
In practice, I would like to run for M and N each be of the order of 2E4, meaning up to 4E8 values of r - which would mean 3 GB of floats (assuming 8 Bytes/float).
For this calculation, I have written the python code below.
The idea is to iterate over m and n, and for each new m/n, insert it in the right place with its probability if it isn't there yet, otherwise add its probability to the existing number. My assumption is that it is easier to sort things on the way instead of waiting until the end.
The cases related to 0 are added at the end of the loop.
I am using the Fraction class since we are dealing with fractions.
The code also tracks the multiplicity of each unique value of m/n.
I have tested up to M=N=100, and things are quite slow. Are there better approaches to the question, or more efficient ways to tackle the code?
Timing:
M=N=30: 1 s
M=N=50: 6 s
M=N=80: 30 s
M=N=100: 82 s
import numpy as np
from fractions import Fraction
import time # For timiing
start_time = time.time() # Timing
M, N = 6, 4
mList, nList = np.arange(1, M+1), np.arange(1, N+1) # From 1 to M inclusive, deal with 0 later
mProbList, nProbList = [1/(M+1)]*(M), [1/(N+1)]*(N) # Probabilities, here assumed equal (not general case)
# Deal with mn=0 later
pmZero, pnZero = 1/(M+1), 1/(N+1) # P(m=0) and P(n=0)
pNaN = pmZero * pnZero # P(0/0) = P(m=0)P(n=0)
pZero = pmZero * (1 - pnZero) # P(0) = P(m=0)P(n!=0)
pInf = pnZero * (1 - pmZero) # P(inf) = P(m!=0)P(n=0)
# Main list of r=m/n, P(r) and mult(r)
# Start with first line, m=1
rList = [Fraction(mList[0], n) for n in nList[::-1]] # Smallest first
rProbList = [mProbList[0] * nP for nP in nProbList[::-1]] # Start with first line
rMultList = [1] * len(rList) # Multiplicity of each element
# Main loop
for m, mP in zip(mList[1:], mProbList[1:]):
for n, nP in zip(nList[::-1], nProbList[::-1]): # Pick an n value
r, rP, rMult = Fraction(m, n), mP*nP, 1
for i in range(len(rList)-1): # See where it fits in existing list
if r < rList[i]:
rList.insert(i, r)
rProbList.insert(i, rP)
rMultList.insert(i, 1)
break
elif r == rList[i]:
rProbList[i] += rP
rMultList[i] += 1
break
elif r < rList[i+1]:
rList.insert(i+1, r)
rProbList.insert(i+1, rP)
rMultList.insert(i+1, 1)
break
elif r == rList[i+1]:
rProbList[i+1] += rP
rMultList[i+1] += 1
break
if r > rList[-1]:
rList.append(r)
rProbList.append(rP)
rMultList.append(1)
break
# Deal with 0
rList.insert(0, Fraction(0, 1))
rProbList.insert(0, pZero)
rMultList.insert(0, N)
# Deal with infty
rList.append(np.Inf)
rProbList.append(pInf)
rMultList.append(M)
# Deal with undefined case
rList.append(np.NAN)
rProbList.append(pNaN)
rMultList.append(1)
print(".... done in %s seconds." % round(time.time() - start_time, 2))
print("************** Final list\nr", 'Prob', 'Mult')
for r, rP, rM in zip(rList, rProbList, rMultList): print(r, rP, rM)
print("************** Checks")
print("mList", mList, 'nList', nList)
print("Sum of proba = ", np.sum(rProbList))
print("Sum of multi = ", np.sum(rMultList), "\t(M+1)*(N+1) = ", (M+1)*(N+1))
Based on the suggestion of #Prune, and on this thread about merging lists of tuples, I have modified the code as below. It's a lot easier to read, and runs about an order of magnitude faster for N=M=80 (I have omitted dealing with 0 - would be done same way as in original post). I assume there may be ways to tweak the merge and conversion back to lists further yet.
# Do calculations
data = [(Fraction(m, n), mProb(m) * nProb(n)) for n in range(1, N+1) for m in range(1, M+1)]
data.sort()
# Merge duplicates using a dictionary
d = {}
for r, p in data:
if not (r in d): d[r] = [0, 0]
d[r][0] += p
d[r][1] += 1
# Convert back to lists
rList, rProbList, rMultList = [], [], []
for k in d:
rList.append(k)
rProbList.append(d[k][0])
rMultList.append(d[k][1])
I expect that "things are quite slow" because you've chosen a known inefficient sort. A single list insertion is O(K) (later list elements have to be bumped over, and there is added storage allocation on a regular basis). Thus a full-list insertion sort is O(K^2). For your notation, that is O((M*N)^2).
If you want any sort of reasonable performance, research and use the best-know methods. The most straightforward way to do this is to make your non-exception results as a simple list comprehension, and use the built-in sort for your penultimate list. Simply append your n=0 cases, and you're done in O(K log K) time.
I the expression below, I've assumed functions for m and n probabilities.
This is a notational convenience; you know how to directly compute them, and can substitute those expressions if you wish.
data = [ (mProb(m) * nProb(n), Fraction(m, n))
for n in range(1, N+1)
for m in range(0, M+1) ]
data.sort()
data.extend([ # generate your "zero" cases here ])
The usual saying is that string comparison must be done in constant time when checking things like password or hashes, and thus, it is recommended to avoid a == b.
However, I run the follow script and the results don't support the hypothesis that a==b short circuit on the first non-identical character.
from time import perf_counter_ns
import random
def timed_cmp(a, b):
start = perf_counter_ns()
a == b
end = perf_counter_ns()
return end - start
def n_timed_cmp(n, a, b):
"average time for a==b done n times"
ts = [timed_cmp(a, b) for _ in range(n)]
return sum(ts) / len(ts)
def check_cmp_time():
random.seed(123)
# generate a random string of n characters
n = 2 ** 8
s = "".join([chr(random.randint(ord("a"), ord("z"))) for _ in range(n)])
# generate a list of strings, which all differs from the original string
# by one character, at a different position
# only do that for the first 50 char, it's enough to get data
diffs = [s[:i] + "A" + s[i+1:] for i in range(min(50, n))]
timed = [(i, n_timed_cmp(10000, s, d)) for (i, d) in enumerate(diffs)]
sorted_timed = sorted(timed, key=lambda t: t[1])
# print the 10 fastest
for x in sorted_timed[:10]:
i, t = x
print("{}\t{:3f}".format(i, t))
print("---")
i, t = timed[0]
print("{}\t{:3f}".format(i, t))
i, t = timed[1]
print("{}\t{:3f}".format(i, t))
if __name__ == "__main__":
check_cmp_time()
Here is the result of a run, re-running the script gives slightly different results, but nothing satisfactory.
# ran with cpython 3.8.3
6 78.051700
1 78.203200
15 78.222700
14 78.384800
11 78.396300
12 78.441800
9 78.476900
13 78.519000
8 78.586200
3 78.631500
---
0 80.691100
1 78.203200
I would've expected that the fastest comparison would be where the first differing character is at the beginning of the string, but it's not what I get.
Any idea what's going on ???
There's a difference, you just don't see it on such small strings. Here's a small patch to apply to your code, so I use longer strings, and I do 10 checks by putting the A at a place, evenly spaced in the original string, from the beginning to the end, I mean, like this:
A_______________________________________________________________
______A_________________________________________________________
____________A___________________________________________________
__________________A_____________________________________________
________________________A_______________________________________
______________________________A_________________________________
____________________________________A___________________________
__________________________________________A_____________________
________________________________________________A_______________
______________________________________________________A_________
____________________________________________________________A___
## -15,13 +15,13 ## def n_timed_cmp(n, a, b):
def check_cmp_time():
random.seed(123)
# generate a random string of n characters
- n = 2 ** 8
+ n = 2 ** 16
s = "".join([chr(random.randint(ord("a"), ord("z"))) for _ in range(n)])
# generate a list of strings, which all differs from the original string
# by one character, at a different position
# only do that for the first 50 char, it's enough to get data
- diffs = [s[:i] + "A" + s[i+1:] for i in range(min(50, n))]
+ diffs = [s[:i] + "A" + s[i+1:] for i in range(0, n, n // 10)]
timed = [(i, n_timed_cmp(10000, s, d)) for (i, d) in enumerate(diffs)]
sorted_timed = sorted(timed, key=lambda t: t[1])
and you'll get:
0 122.621000
1 213.465700
2 380.214100
3 460.422000
5 694.278700
4 722.010000
7 894.630300
6 1020.722100
9 1149.473000
8 1341.754500
---
0 122.621000
1 213.465700
Note that with your example, with only 2**8 characters, it's already noticable, apply this patch:
## -21,7 +21,7 ## def check_cmp_time():
# generate a list of strings, which all differs from the original string
# by one character, at a different position
# only do that for the first 50 char, it's enough to get data
- diffs = [s[:i] + "A" + s[i+1:] for i in range(min(50, n))]
+ diffs = [s[:i] + "A" + s[i+1:] for i in [0, n - 1]]
timed = [(i, n_timed_cmp(10000, s, d)) for (i, d) in enumerate(diffs)]
sorted_timed = sorted(timed, key=lambda t: t[1])
to only keep the two extreme cases (first letter change vs last letter change) and you'll get:
$ python3 cmp.py
0 124.131800
1 135.566000
Numbers may vary, but most of the time test 0 is a tad faster that test 1.
To isolate more precisely which caracter is modified, it's possible as long as the memcmp does it character by character, so as long as it does not use integer comparisons, typically on the last character if they get misaligned, or on really short strings, like 8 char string, as I demo here:
from time import perf_counter_ns
from statistics import median
import random
def check_cmp_time():
random.seed(123)
# generate a random string of n characters
n = 8
s = "".join([chr(random.randint(ord("a"), ord("z"))) for _ in range(n)])
# generate a list of strings, which all differs from the original string
# by one character, at a different position
# only do that for the first 50 char, it's enough to get data
diffs = [s[:i] + "A" + s[i + 1 :] for i in range(n)]
values = {x: [] for x in range(n)}
for _ in range(10_000_000):
for i, diff in enumerate(diffs):
start = perf_counter_ns()
s == diff
values[i].append(perf_counter_ns() - start)
timed = [[k, median(v)] for k, v in values.items()]
sorted_timed = sorted(timed, key=lambda t: t[1])
# print the 10 fastest
for x in sorted_timed[:10]:
i, t = x
print("{}\t{:3f}".format(i, t))
print("---")
i, t = timed[0]
print("{}\t{:3f}".format(i, t))
i, t = timed[1]
print("{}\t{:3f}".format(i, t))
if __name__ == "__main__":
check_cmp_time()
Which gives me:
1 221.000000
2 222.000000
3 223.000000
4 223.000000
5 223.000000
6 223.000000
7 223.000000
0 241.000000
The differences are so small, Python and perf_counter_ns may no longer be the right tools here.
See, to know why it doesn't short circuit, you'll have to do some digging. The simple answer is, of course, it doesn't short circuit because the standard doesn't specify so. But you might think, "Why wouldn't the implementations choose to short circuit? Surely, It must be faster!". Not quite.
Let's take a look at cpython, for obvious reasons. Look at the code for unicode_compare_eq function defined in unicodeobject.c
static int
unicode_compare_eq(PyObject *str1, PyObject *str2)
{
int kind;
void *data1, *data2;
Py_ssize_t len;
int cmp;
len = PyUnicode_GET_LENGTH(str1);
if (PyUnicode_GET_LENGTH(str2) != len)
return 0;
kind = PyUnicode_KIND(str1);
if (PyUnicode_KIND(str2) != kind)
return 0;
data1 = PyUnicode_DATA(str1);
data2 = PyUnicode_DATA(str2);
cmp = memcmp(data1, data2, len * kind);
return (cmp == 0);
}
(Note: This function is actually called after deducing that str1 and str2 are not the same object - if they are - well that's just a simple True immediately)
Focus on this line specifically-
cmp = memcmp(data1, data2, len * kind);
Ahh, we're back at another cross road. Does memcmp short circuit? The C standard does not specify such a requirement. As seen in the opengroup docs and also in Section 7.24.4.1 of the C Standard Draft
7.24.4.1 The memcmp function
Synopsis
#include <string.h>
int memcmp(const void *s1, const void *s2, size_t n);
Description
The memcmp function compares the first n characters of the object pointed to by s1 to
the first n characters of the object pointed to by s2.
Returns
The memcmp function returns an integer greater than, equal to, or less than zero,
accordingly as the object pointed to by s1 is greater than, equal to, or less than the object pointed to by s2.
Most Some C implementations (including glibc) choose to not short circuit. But why? are we missing something, why would you not short circuit?
Because the comparison they use isn't might not be as naive as a byte by byte by check. The standard does not require the objects to be compared byte by byte. Therein lies the chance of optimization.
What glibc does, is that it compares elements of type unsigned long int instead of just singular bytes represented by unsigned char. Check out the implementation
There's a lot more going under the hood - a discussion far outside the scope of this question, after all this isn't even tagged as a C question ;). Though I found that this answer may be worth a look. But just know, the optimization is there, just in a much different form than the approach that may come in mind at first glance.
Edit: Fixed wrong function link
Edit: As #Konrad Rudolph has stated, glibc memcmp does apparently short circuit. I've been misinformed.
I want to get the length of a string including a part of the string that represents its own length without padding or using structs or anything like that that forces fixed lengths.
So for example I want to be able to take this string as input:
"A string|"
And return this:
"A string|11"
On the basis of the OP tolerating such an approach (and to provide an implementation technique for the eventual python answer), here's a solution in Java.
final String s = "A String|";
int n = s.length(); // `length()` returns the length of the string.
String t; // the result
do {
t = s + n; // append the stringified n to the original string
if (n == t.length()){
return t; // string length no longer changing; we're good.
}
n = t.length(); // n must hold the total length
} while (true); // round again
The problem of, course, is that in appending n, the string length changes. But luckily, the length only ever increases or stays the same. So it will converge very quickly: due to the logarithmic nature of the length of n. In this particular case, the attempted values of n are 9, 10, and 11. And that's a pernicious case.
A simple solution is :
def addlength(string):
n1=len(string)
n2=len(str(n1))+n1
n2 += len(str(n2))-len(str(n1)) # a carry can arise
return string+str(n2)
Since a possible carry will increase the length by at most one unit.
Examples :
In [2]: addlength('a'*8)
Out[2]: 'aaaaaaaa9'
In [3]: addlength('a'*9)
Out[3]: 'aaaaaaaaa11'
In [4]: addlength('a'*99)
Out[4]: 'aaaaa...aaa102'
In [5]: addlength('a'*999)
Out[5]: 'aaaa...aaa1003'
Here is a simple python port of Bathsheba's answer :
def str_len(s):
n = len(s)
t = ''
while True:
t = s + str(n)
if n == len(t):
return t
n = len(t)
This is a much more clever and simple way than anything I was thinking of trying!
Suppose you had s = 'abcdefgh|, On the first pass through, t = 'abcdefgh|9
Since n != len(t) ( which is now 10 ) it goes through again : t = 'abcdefgh|' + str(n) and str(n)='10' so you have abcdefgh|10 which is still not quite right! Now n=len(t) which is finally n=11 you get it right then. Pretty clever solution!
It is a tricky one, but I think I've figured it out.
Done in a hurry in Python 2.7, please fully test - this should handle strings up to 998 characters:
import sys
orig = sys.argv[1]
origLen = len(orig)
if (origLen >= 98):
extra = str(origLen + 3)
elif (origLen >= 8):
extra = str(origLen + 2)
else:
extra = str(origLen + 1)
final = orig + extra
print final
Results of very brief testing
C:\Users\PH\Desktop>python test.py "tiny|"
tiny|6
C:\Users\PH\Desktop>python test.py "myString|"
myString|11
C:\Users\PH\Desktop>python test.py "myStringWith98Characters.........................................................................|"
myStringWith98Characters.........................................................................|101
Just find the length of the string. Then iterate through each value of the number of digits the length of the resulting string can possibly have. While iterating, check if the sum of the number of digits to be appended and the initial string length is equal to the length of the resulting string.
def get_length(s):
s = s + "|"
result = ""
len_s = len(s)
i = 1
while True:
candidate = len_s + i
if len(str(candidate)) == i:
result = s + str(len_s + i)
break
i += 1
This code gives the result.
I used a few var, but at the end it shows the output you want:
def len_s(s):
s = s + '|'
b = len(s)
z = s + str(b)
length = len(z)
new_s = s + str(length)
new_len = len(new_s)
return s + str(new_len)
s = "A string"
print len_s(s)
Here's a direct equation for this (so it's not necessary to construct the string). If s is the string, then the length of the string including the length of the appended length will be:
L1 = len(s) + 1 + int(log10(len(s) + 1 + int(log10(len(s)))))
The idea here is that a direct calculation is only problematic when the appended length will push the length past a power of ten; that is, at 9, 98, 99, 997, 998, 999, 9996, etc. To work this through, 1 + int(log10(len(s))) is the number of digits in the length of s. If we add that to len(s), then 9->10, 98->100, 99->101, etc, but still 8->9, 97->99, etc, so we can push past the power of ten exactly as needed. That is, adding this produces a number with the correct number of digits after the addition. Then do the log again to find the length of that number and that's the answer.
To test this:
from math import log10
def find_length(s):
L1 = len(s) + 1 + int(log10(len(s) + 1 + int(log10(len(s)))))
return L1
# test, just looking at lengths around 10**n
for i in range(9):
for j in range(30):
L = abs(10**i - j + 10) + 1
s = "a"*L
x0 = find_length(s)
new0 = s+`x0`
if len(new0)!=x0:
print "error", len(s), x0, log10(len(s)), log10(x0)
My problem is as follows:
having file with list of intervals:
1 5
2 8
9 12
20 30
And a range of
0 200
I would like to do such an intersection that will report the positions [start end] between my intervals inside the given range.
For example:
8 9
12 20
30 200
Beside any ideas how to bite this, would be also nice to read some thoughts on optimization, since as always the input files are going to be huge.
this solution works as long the intervals are ordered by the start point and does not require to create a list as big as the total range.
code
with open("0.txt") as f:
t=[x.rstrip("\n").split("\t") for x in f.readlines()]
intervals=[(int(x[0]),int(x[1])) for x in t]
def find_ints(intervals, mn, mx):
next_start = mn
for x in intervals:
if next_start < x[0]:
yield next_start,x[0]
next_start = x[1]
elif next_start < x[1]:
next_start = x[1]
if next_start < mx:
yield next_start, mx
print list(find_ints(intervals, 0, 200))
output:
(in the case of the example you gave)
[(0, 1), (8, 9), (12, 20), (30, 200)]
Rough algorithm:
create an array of booleans, all set to false seen = [False]*200
Iterate over the input file, for each line start end set seen[start] .. seen[end] to be True
Once done, then you can trivially walk the array to find the unused intervals.
In terms of optimisations, if the list of input ranges is sorted on start number, then you can track the highest seen number and use that to filter ranges as they are processed -
e.g. something like
for (start,end) in input:
if end<=lowest_unseen:
next
if start<lowest_unseen:
start=lowest_unseen
...
which (ignoring the cost of the original sort) should make the whole thing O(n) - you go through the array once to tag seen/unseen and once to output unseens.
Seems I'm feeling nice. Here is the (unoptimised) code, assuming your input file is called input
seen = [False]*200
file = open('input','r')
rows = file.readlines()
for row in rows:
(start,end) = row.split(' ')
print "%s %s" % (start,end)
for x in range( int(start)-1, int(end)-1 ):
seen[x] = True
print seen[0:10]
in_unseen_block=False
start=1
for x in range(1,200):
val=seen[x-1]
if val and not in_unseen_block:
continue
if not val and in_unseen_block:
continue
# Must be at a change point.
if val:
# we have reached the end of the block
print "%s %s" % (start,x)
in_unseen_block = False
else:
# start of new block
start = x
in_unseen_block = True
# Handle end block
if in_unseen_block:
print "%s %s" % (start, 200)
I'm leaving the optimizations as an exercise for the reader.
If you make a note every time that one of your input intervals either opens or closes, you can do what you want by putting together the keys of opens and closes, sort into an ordered set, and you'll be able to essentially think, "okay, let's say that each adjacent pair of numbers forms an interval. Then I can focus all of my logic on these intervals as discrete chunks."
myRange = range(201)
intervals = [(1,5), (2,8), (9,12), (20,30)]
opens = {}
closes = {}
def open(index):
if index not in opens:
opens[index] = 0
opens[index] += 1
def close(index):
if index not in closes:
closes[index] = 0
closes[index] += 1
for start, end in intervals:
if end > start: # Making sure to exclude empty intervals, which can be problematic later
open(start)
close(end)
# Sort all the interval-endpoints that we really need to look at
oset = {0:None, 200:None}
for k in opens.keys():
oset[k] = None
for k in closes.keys():
oset[k] = None
relevant_indices = sorted(oset.keys())
# Find the clear ranges
state = 0
results = []
for i in range(len(relevant_indices) - 1):
start = relevant_indices[i]
end = relevant_indices[i+1]
start_state = state
if start in opens:
start_state += opens[start]
if start in closes:
start_state -= closes[start]
end_state = start_state
if end in opens:
end_state += opens[end]
if end in closes:
end_state -= closes[end]
state = end_state
if start_state == 0:
result_start = start
result_end = end
results.append((result_start, result_end))
for start, end in results:
print(str(start) + " " + str(end))
This outputs:
0 1
8 9
12 20
30 200
The intervals don't need to be sorted.
This question seems to be a duplicate of Merging intervals in Python.
If I understood well the problem, you have a list of intervals (1 5; 2 8; 9 12; 20 30) and a range (0 200), and you want to get the positions outside your intervals, but inside given range. Right?
There's a Python library that can help you on that: python-intervals (also available from PyPI using pip). Disclaimer: I'm the maintainer of that library.
Assuming you import this library as follows:
import intervals as I
It's quite easy to get your answer. Basically, you first want to create a disjunction of intervals based on the ones you provide:
inters = I.closed(1, 5) | I.closed(2, 8) | I.closed(9, 12) | I.closed(20, 30)
Then you compute the complement of these intervals, to get everything that is "outside":
compl = ~inters
Then you create the union with [0, 200], as you want to restrict the points to that interval:
print(compl & I.closed(0, 200))
This results in:
[0,1) | (8,9) | (12,20) | (30,200]
From Section 15.2 of Programming Pearls
The C codes can be viewed here: http://www.cs.bell-labs.com/cm/cs/pearls/longdup.c
When I implement it in Python using suffix-array:
example = open("iliad10.txt").read()
def comlen(p, q):
i = 0
for x in zip(p, q):
if x[0] == x[1]:
i += 1
else:
break
return i
suffix_list = []
example_len = len(example)
idx = list(range(example_len))
idx.sort(cmp = lambda a, b: cmp(example[a:], example[b:])) #VERY VERY SLOW
max_len = -1
for i in range(example_len - 1):
this_len = comlen(example[idx[i]:], example[idx[i+1]:])
print this_len
if this_len > max_len:
max_len = this_len
maxi = i
I found it very slow for the idx.sort step. I think it's slow because Python need to pass the substring by value instead of by pointer (as the C codes above).
The tested file can be downloaded from here
The C codes need only 0.3 seconds to finish.
time cat iliad10.txt |./longdup
On this the rest of the Achaeans with one voice were for
respecting the priest and taking the ransom that he offered; but
not so Agamemnon, who spoke fiercely to him and sent him roughly
away.
real 0m0.328s
user 0m0.291s
sys 0m0.006s
But for Python codes, it never ends on my computer (I waited for 10 minutes and killed it)
Does anyone have ideas how to make the codes efficient? (For example, less than 10 seconds)
My solution is based on Suffix arrays. It is constructed by Prefix doubling the Longest common prefix. The worst-case complexity is O(n (log n)^2). The file "iliad.mb.txt" takes 4 seconds on my laptop. The longest_common_substring function is short and can be easily modified, e.g. for searching the 10 longest non-overlapping substrings. This Python code is faster than the original C code from the question, if duplicate strings are longer than 10000 characters.
from itertools import groupby
from operator import itemgetter
def longest_common_substring(text):
"""Get the longest common substrings and their positions.
>>> longest_common_substring('banana')
{'ana': [1, 3]}
>>> text = "not so Agamemnon, who spoke fiercely to "
>>> sorted(longest_common_substring(text).items())
[(' s', [3, 21]), ('no', [0, 13]), ('o ', [5, 20, 38])]
This function can be easy modified for any criteria, e.g. for searching ten
longest non overlapping repeated substrings.
"""
sa, rsa, lcp = suffix_array(text)
maxlen = max(lcp)
result = {}
for i in range(1, len(text)):
if lcp[i] == maxlen:
j1, j2, h = sa[i - 1], sa[i], lcp[i]
assert text[j1:j1 + h] == text[j2:j2 + h]
substring = text[j1:j1 + h]
if not substring in result:
result[substring] = [j1]
result[substring].append(j2)
return dict((k, sorted(v)) for k, v in result.items())
def suffix_array(text, _step=16):
"""Analyze all common strings in the text.
Short substrings of the length _step a are first pre-sorted. The are the
results repeatedly merged so that the garanteed number of compared
characters bytes is doubled in every iteration until all substrings are
sorted exactly.
Arguments:
text: The text to be analyzed.
_step: Is only for optimization and testing. It is the optimal length
of substrings used for initial pre-sorting. The bigger value is
faster if there is enough memory. Memory requirements are
approximately (estimate for 32 bit Python 3.3):
len(text) * (29 + (_size + 20 if _size > 2 else 0)) + 1MB
Return value: (tuple)
(sa, rsa, lcp)
sa: Suffix array for i in range(1, size):
assert text[sa[i-1]:] < text[sa[i]:]
rsa: Reverse suffix array for i in range(size):
assert rsa[sa[i]] == i
lcp: Longest common prefix for i in range(1, size):
assert text[sa[i-1]:sa[i-1]+lcp[i]] == text[sa[i]:sa[i]+lcp[i]]
if sa[i-1] + lcp[i] < len(text):
assert text[sa[i-1] + lcp[i]] < text[sa[i] + lcp[i]]
>>> suffix_array(text='banana')
([5, 3, 1, 0, 4, 2], [3, 2, 5, 1, 4, 0], [0, 1, 3, 0, 0, 2])
Explanation: 'a' < 'ana' < 'anana' < 'banana' < 'na' < 'nana'
The Longest Common String is 'ana': lcp[2] == 3 == len('ana')
It is between tx[sa[1]:] == 'ana' < 'anana' == tx[sa[2]:]
"""
tx = text
size = len(tx)
step = min(max(_step, 1), len(tx))
sa = list(range(len(tx)))
sa.sort(key=lambda i: tx[i:i + step])
grpstart = size * [False] + [True] # a boolean map for iteration speedup.
# It helps to skip yet resolved values. The last value True is a sentinel.
rsa = size * [None]
stgrp, igrp = '', 0
for i, pos in enumerate(sa):
st = tx[pos:pos + step]
if st != stgrp:
grpstart[igrp] = (igrp < i - 1)
stgrp = st
igrp = i
rsa[pos] = igrp
sa[i] = pos
grpstart[igrp] = (igrp < size - 1 or size == 0)
while grpstart.index(True) < size:
# assert step <= size
nextgr = grpstart.index(True)
while nextgr < size:
igrp = nextgr
nextgr = grpstart.index(True, igrp + 1)
glist = []
for ig in range(igrp, nextgr):
pos = sa[ig]
if rsa[pos] != igrp:
break
newgr = rsa[pos + step] if pos + step < size else -1
glist.append((newgr, pos))
glist.sort()
for ig, g in groupby(glist, key=itemgetter(0)):
g = [x[1] for x in g]
sa[igrp:igrp + len(g)] = g
grpstart[igrp] = (len(g) > 1)
for pos in g:
rsa[pos] = igrp
igrp += len(g)
step *= 2
del grpstart
# create LCP array
lcp = size * [None]
h = 0
for i in range(size):
if rsa[i] > 0:
j = sa[rsa[i] - 1]
while i != size - h and j != size - h and tx[i + h] == tx[j + h]:
h += 1
lcp[rsa[i]] = h
if h > 0:
h -= 1
if size > 0:
lcp[0] = 0
return sa, rsa, lcp
I prefer this solution over more complicated O(n log n) because Python has a very fast list sorting algorithm (Timsort). Python's sort is probably faster than necessary linear time operations in the method from that article, that should be O(n) under very special presumptions of random strings together with a small alphabet (typical for DNA genome analysis). I read in Gog 2011 that worst-case O(n log n) of my algorithm can be in practice faster than many O(n) algorithms that cannot use the CPU memory cache.
The code in another answer based on grow_chains is 19 times slower than the original example from the question, if the text contains a repeated string 8 kB long. Long repeated texts are not typical for classical literature, but they are frequent e.g. in "independent" school homework collections. The program should not freeze on it.
I wrote an example and tests with the same code for Python 2.7, 3.3 - 3.6.
The translation of the algorithm into Python:
from itertools import imap, izip, starmap, tee
from os.path import commonprefix
def pairwise(iterable): # itertools recipe
a, b = tee(iterable)
next(b, None)
return izip(a, b)
def longest_duplicate_small(data):
suffixes = sorted(data[i:] for i in xrange(len(data))) # O(n*n) in memory
return max(imap(commonprefix, pairwise(suffixes)), key=len)
buffer() allows to get a substring without copying:
def longest_duplicate_buffer(data):
n = len(data)
sa = sorted(xrange(n), key=lambda i: buffer(data, i)) # suffix array
def lcp_item(i, j): # find longest common prefix array item
start = i
while i < n and data[i] == data[i + j - start]:
i += 1
return i - start, start
size, start = max(starmap(lcp_item, pairwise(sa)), key=lambda x: x[0])
return data[start:start + size]
It takes 5 seconds on my machine for the iliad.mb.txt.
In principle it is possible to find the duplicate in O(n) time and O(n) memory using a suffix array augmented with a lcp array.
Note: *_memoryview() is deprecated by *_buffer() version
More memory efficient version (compared to longest_duplicate_small()):
def cmp_memoryview(a, b):
for x, y in izip(a, b):
if x < y:
return -1
elif x > y:
return 1
return cmp(len(a), len(b))
def common_prefix_memoryview((a, b)):
for i, (x, y) in enumerate(izip(a, b)):
if x != y:
return a[:i]
return a if len(a) < len(b) else b
def longest_duplicate(data):
mv = memoryview(data)
suffixes = sorted((mv[i:] for i in xrange(len(mv))), cmp=cmp_memoryview)
result = max(imap(common_prefix_memoryview, pairwise(suffixes)), key=len)
return result.tobytes()
It takes 17 seconds on my machine for the iliad.mb.txt. The result is:
On this the rest of the Achaeans with one voice were for respecting
the priest and taking the ransom that he offered; but not so Agamemnon,
who spoke fiercely to him and sent him roughly away.
I had to define custom functions to compare memoryview objects because memoryview comparison either raises an exception in Python 3 or produces wrong result in Python 2:
>>> s = b"abc"
>>> memoryview(s[0:]) > memoryview(s[1:])
True
>>> memoryview(s[0:]) < memoryview(s[1:])
True
Related questions:
Find the longest repeating string and the number of times it repeats in a given string
finding long repeated substrings in a massive string
The main problem seems to be that python does slicing by copy: https://stackoverflow.com/a/5722068/538551
You'll have to use a memoryview instead to get a reference instead of a copy. When I did this, the program hung after the idx.sort function (which was very fast).
I'm sure with a little work, you can get the rest working.
Edit:
The above change will not work as a drop-in replacement because cmp does not work the same way as strcmp. For example, try the following C code:
#include <stdio.h>
#include <string.h>
int main() {
char* test1 = "ovided by The Internet Classics Archive";
char* test2 = "rovided by The Internet Classics Archive.";
printf("%d\n", strcmp(test1, test2));
}
And compare the result to this python:
test1 = "ovided by The Internet Classics Archive";
test2 = "rovided by The Internet Classics Archive."
print(cmp(test1, test2))
The C code prints -3 on my machine while the python version prints -1. It looks like the example C code is abusing the return value of strcmp (it IS used in qsort after all). I couldn't find any documentation on when strcmp will return something other than [-1, 0, 1], but adding a printf to pstrcmp in the original code showed a lot of values outside of that range (3, -31, 5 were the first 3 values).
To make sure that -3 wasn't some error code, if we reverse test1 and test2, we'll get 3.
Edit:
The above is interesting trivia, but not actually correct in terms of affecting either chunks of code. I realized this just as I shut my laptop and left a wifi zone... Really should double check everything before I hit Save.
FWIW, cmp most certainly works on memoryview objects (prints -1 as expected):
print(cmp(memoryview(test1), memoryview(test2)))
I'm not sure why the code isn't working as expected. Printing out the list on my machine does not look as expected. I'll look into this and try to find a better solution instead of grasping at straws.
This version takes about 17 secs on my circa-2007 desktop using totally different algorithm:
#!/usr/bin/env python
ex = open("iliad.mb.txt").read()
chains = dict()
# populate initial chains dictionary
for (a,b) in enumerate(zip(ex,ex[1:])) :
s = ''.join(b)
if s not in chains :
chains[s] = list()
chains[s].append(a)
def grow_chains(chains) :
new_chains = dict()
for (string,pos) in chains :
offset = len(string)
for p in pos :
if p + offset >= len(ex) : break
# add one more character
s = string + ex[p + offset]
if s not in new_chains :
new_chains[s] = list()
new_chains[s].append(p)
return new_chains
# grow and filter, grow and filter
while len(chains) > 1 :
print 'length of chains', len(chains)
# remove chains that appear only once
chains = [(i,chains[i]) for i in chains if len(chains[i]) > 1]
print 'non-unique chains', len(chains)
print [i[0] for i in chains[:3]]
chains = grow_chains(chains)
The basic idea is to create a list of substrings and positions where they occure, thus eliminating the need to compare same strings again and again. The resulting list look like [('ind him, but', [466548, 739011]), (' bulwark bot', [428251, 428924]), (' his armour,', [121559, 124919, 193285, 393566, 413634, 718953, 760088])]. Unique strings are removed. Then every list member grows by 1 character and new list is created. Unique strings are removed again. And so on and so forth...