Is there any ways to make this more efficient? - python-3.x

I have 24 more attempts to submit this task. I spent hours and my brain does not work anymore. I am a beginner with Python can you please help to figure out what is wrong? I would love to see the correct code if possible.
Here is the task itself and the code I wrote below.
Note that you can have access to all standard modules/packages/libraries of your language. But there is no access to additional libraries (numpy in python, boost in c++, etc).
You are given a content of CSV-file with information about set of trades. It contains the following columns:
TIME - Timestamp of a trade in format Hour:Minute:Second.Millisecond
PRICE - Price of one share
SIZE - Count of shares executed in this trade
EXCHANGE - The exchange that executed this trade
For each exchange find the one minute-window during which the largest number of trades took place on this exchange.
Note that:
You need to send source code of your program.
You have only 25 attempts to submit a solutions for this task.
You have access to all standart modules/packages/libraries of your language. But there is no access to additional libraries (numpy in python, boost in c++, etc).
Input format
Input contains several lines. You can read it from standart input or file “trades.csv”
Each line contains information about one trade: TIME, PRICE, SIZE and EXCHANGE. Numbers are separated by comma.
Lines are listed in ascending order of timestamps. Several lines can contain the same timestamp.
Size of input file does not exceed 5 MB.
See the example below to understand the exact input format.
Output format
If input contains information about k exchanges, print k lines to standart output.
Each line should contain the only number — maximum number of trades during one minute-window.
You should print answers for exchanges in lexicographical order of their names.
Sample
Input Output
09:30:01.034,36.99,100,V
09:30:55.000,37.08,205,V
09:30:55.554,36.90,54,V
09:30:55.556,36.91,99,D
09:31:01.033,36.94,100,D
09:31:01.034,36.95,900,V
2
3
Notes
In the example four trades were executed on exchange “V” and two trades were executed on exchange “D”. Not all of the “V”-trades fit in one minute-window, so the answer for “V” is three.
X = []
with open('trades.csv', 'r') as tr:
for line in tr:
line = line.strip('\xef\xbb\xbf\r\n ')
X.append(line.split(','))
dex = {}
for item in X:
dex[item[3]] = []
for item in X:
dex[item[3]].append(float(item[0][:2])*60.+float(item[0][3:5])+float(item[0][6:8])/60.+float(item[0][9:])/60000.)
for item in dex:
count = 1
ccount = 1
if dex[item][len(dex[item])-1]-dex[item][0] <1:
count = len(dex[item])
else:
for t in range(len(dex[item])-1):
for tt in range(len(dex[item])-t-1):
if dex[item][tt+t+1]-dex[item][t] <1:
ccount += 1
else: break
if ccount>count:
count=ccount
ccount=1
print(count)

First of all it is not necessary to use datetime and csv modules for such a simple case (like in Ed-Ward's example).
If we remove colon and dot signs from the time strings it could be converted to int() directly - easier way than you tried in your example.
CSV features like dialect and special formatting not used so i suggest to use simple split(",")
Now about efficiency. Efficiency means time complexity.
The more times you go through your array with dates from the beginning to the end, the more complicated the algorithm becomes.
So our goal is to minimize cycles count, best to make only one pass by all rows and especially avoid nested loops and passing through collections from beginning to the end.
For such a task it is better to use deque, instead of tuple or list, because you can pop() first element and append last element with complexity of O(1).
Just append every time for needed exchange to the end of the exchange's queue until difference between current and first elements becomes more than 1 minute. Then just remove first element with popleft() and continue comparison. After whole file done - length of each queue will be the max 1min window.
Example with linear time complexity O(n):
from collections import deque
ex_list = {}
s = open("trades.csv").read().replace(":", "").replace(".", "")
for line in s.splitlines():
s = line.split(",")
curr_tm = int(s[0])
curr_ex = s[3]
if curr_ex not in ex_list:
ex_list[curr_ex] = deque()
ex_list[curr_ex].append(curr_tm)
if curr_tm >= ex_list[curr_ex][0] + 100000:
ex_list[curr_ex].popleft()
print("\n".join([str(len(ex_list[k])) for k in sorted(ex_list.keys())]))

This code should work:
import csv
import datetime
diff = datetime.timedelta(minutes=1)
def date_calc(start, dates):
for i, date in enumerate(dates):
if date >= start + diff:
return i
return i + 1
exchanges = {}
with open("trades.csv") as csvfile:
reader = csv.reader(csvfile)
for row in reader:
this_exchange = row[3]
if this_exchange not in exchanges:
exchanges[this_exchange] = []
time = datetime.datetime.strptime(row[0], "%H:%M:%S.%f")
exchanges[this_exchange].append(time)
ex_max = {}
for name, dates in exchanges.items():
ex_max[name] = 0
for i, d in enumerate(dates):
x = date_calc(d, dates[i:])
if x > ex_max[name]:
ex_max[name] = x
print('\n'.join([str(ex_max[k]) for k in sorted(ex_max.keys())]))
Output:
2
3
( obviously please check it for yourself before uploading it :) )
I think the issue with your current code is that you don't put the output in lexicographical order of their names...
If you want to use your current code, then here is a (hopefully) fixed version:
X = []
with open('trades.csv', 'r') as tr:
for line in tr:
line = line.strip('\xef\xbb\xbf\r\n ')
X.append(line.split(','))
dex = {}
counts = []
for item in X:
dex[item[3]] = []
for item in X:
dex[item[3]].append(float(item[0][:2])*60.+float(item[0][3:5])+float(item[0][6:8])/60.+float(item[0][9:])/60000.)
for item in dex:
count = 1
ccount = 1
if dex[item][len(dex[item])-1]-dex[item][0] <1:
count = len(dex[item])
else:
for t in range(len(dex[item])-1):
for tt in range(len(dex[item])-t-1):
if dex[item][tt+t+1]-dex[item][t] <1:
ccount += 1
else: break
if ccount>count:
count=ccount
ccount=1
counts.append((item, count))
counts.sort(key=lambda x: x[0])
print('\n'.join([str(x[1]) for x in counts]))
Output:
2
3
I do think you can make your life easier in the future by using Python's standard library, though :)

Related

What are faster ways of reading big data set and apply row wise operations other than pandas and dask?

I am working on a code where I need to populate a set of data structure based on each row of a big table. Right now, I am using pandas to read the data and do some elementary data validation preprocess. However, when I get to the rest of process and putting data in the corresponding data structure, it takes considerably long time for the loop to be completed and my data structures gets populated. For example, in the following code I have a table with 15 M records. Table has three columns and I create a foo() object base on each row and add it to a list.
# Profile.csv
# Index | Name | Family| DB
# ---------|------|-------|----------
# 0. | Jane | Doe | 08/23/1977
# ...
# 15000000 | Jhon | Doe | 01/01/2000
class foo():
def __init__(self, name, last, bd):
self.name = name
self.last = last
self.bd = bd
def populate(row, my_list):
my_list.append(foo(*row))
# reading the csv file and formatting the date column
df = pd.read_csv('Profile.csv')
df['DB'] = pd.to_datetime(df['DB'],'%Y-%m-%d')
# using apply to create an foo() object and add it to the list
my_list = []
gf.apply(populate, axis=1, args=(my_list,))
So the after using pandas to convert the string date to the date object, I just need to iterate over the DataFrame to creat my object and add them to the list. This process is very time taking (in my real example it is even taking more time since my data structure is more complex and I have more columns). So, I am wondering what is the best practice in this case to enhance my run time. Should I even use pandas to read my big tables and process through them row by row?
it would be simply faster using a file handle:
input_file = "profile.csv"
sep=";"
my_list = []
with open(input_file) as fh:
cols = {}
for i, col in enumerate(fh.readline().strip().split(sep)):
cols[col] = i
for line in fh:
line = line.strip().split(sep)
date = line[cols["DB"]].split("/")
date = [date[2], date[0], date[1]]
line[cols["DB"]] = "-".join(date)
populate(line, my_list)
There are multiple approaches for this kind of situation, however, the fastest and most effective method is using vectorization if possible. The solution for the example I demonstrated in this post using vectorization could be as follows:
my_list = [foo(*args) for args in zip(df["Name"],df["Family"],df["BD"])]
If the vectorization is not possible, converting the data framce to a dictionary could significantly improve the performance. For the current example if would be something like:
my_list = []
dc = df.to_dict()
for i, j in dc.items():
my_list.append(foo(dc["Name"][i], dc["Family"][i], dc["BD"][i]))
The last solution is particularly very effective if the type of structures and processes are more complex.

Analysis of Eye-Tracking data in python (Eye-link)

I have data from eye-tracking (.edf file - from Eyelink by SR-research). I want to analyse it and get various measures such as fixation, saccade, duration, etc.
Is there an existing package to analyse Eye-Tracking data?
Thanks!
At least for importing the .edf-file into a pandas DF, you can use the following package by Niklas Wilming: https://github.com/nwilming/pyedfread/tree/master/pyedfread
This should already take care of saccades and fixations - have a look at the readme. Once they're in the data frame, you can apply whatever analysis you want to it.
pyeparse seems to be another (yet currently unmaintained as it seems) library that can be used for eyelink data analysis.
Here is a short excerpt from their example:
import numpy as np
import matplotlib.pyplot as plt
import pyeparse as pp
fname = '../pyeparse/tests/data/test_raw.edf'
raw = pp.read_raw(fname)
# visualize initial calibration
raw.plot_calibration(title='5-Point Calibration')
# create heatmap
raw.plot_heatmap(start=3., stop=60.)
EDIT: After I posted my answer I found a nice list compiling lots of potential tools for eyelink edf data analysis: https://github.com/davebraze/FDBeye/wiki/Researcher-Contributed-Eye-Tracking-Tools
Hey the question seems rather old but maybe I can reactivate it, because I am currently facing the same situation.
To start I recommend to convert your .edf to an .asc file. In this way it is easier to read it to get a first impression.
For this there exist many tools, but I used the SR-Research Eyelink Developers Kit (here).
I don't know your setup but the Eyelink 1000 itself detects saccades and fixation. I my case in the .asc file it looks like that:
SFIX L 10350642
10350642 864.3 542.7 2317.0
...
...
10350962 863.2 540.4 2354.0
EFIX L 10350642 10350962 322 863.1 541.2 2339
SSACC L 10350964
10350964 863.4 539.8 2359.0
...
...
10351004 683.4 511.2 2363.0
ESACC L 10350964 10351004 42 863.4 539.8 683.4 511.2 5.79 221
The first number corresponds to the timestamp, the second and third to x-y coordinates and the last is your pupil diameter (what the last numbers after ESACC are, I don't know).
SFIX -> start fixation
EFIX -> end fixation
SSACC -> start saccade
ESACC -> end saccade
You can also check out PyGaze, I haven't worked with it, but searching for a toolbox, this one always popped up.
EDIT
I found this toolbox here. It looks cool and works fine with the example data, but sadly does not work with mine
EDIT No 2
Revisiting this question after working on my own Eyetracking data I thought I might share a function wrote, to work with my data:
def eyedata2pandasframe(directory):
'''
This function takes a directory from which it tries to read in ASCII files containing eyetracking data
It returns eye_data: A pandas dataframe containing data from fixations AND saccades fix_data: A pandas dataframe containing only data from fixations
sac_data: pandas dataframe containing only data from saccades
fixation: numpy array containing information about fixation onsets and offsets
saccades: numpy array containing information about saccade onsets and offsets
blinks: numpy array containing information about blink onsets and offsets
trials: numpy array containing information about trial onsets
'''
eye_data= []
fix_data = []
sac_data = []
data_header = {0: 'TimeStamp',1: 'X_Coord',2: 'Y_Coord',3: 'Diameter'}
event_header = {0: 'Start', 1: 'End'}
start_reading = False
in_blink = False
in_saccade = False
fix_timestamps = []
sac_timestamps = []
blink_timestamps = []
trials = []
sample_rate_info = []
sample_rate = 0
# read the file and store, depending on the messages the data
# we have the following structure:
# a header -- every line starts with a '**'
# a bunch of messages containing information about callibration/validation and so on all starting with 'MSG'
# followed by:
# START 10350638 LEFT SAMPLES EVENTS
# PRESCALER 1
# VPRESCALER 1
# PUPIL AREA
# EVENTS GAZE LEFT RATE 500.00 TRACKING CR FILTER 2
# SAMPLES GAZE LEFT RATE 500.00 TRACKING CR FILTER 2
# followed by the actual data:
# normal data --> [TIMESTAMP]\t [X-Coords]\t [Y-Coords]\t [Diameter]
# Start of EVENTS [BLINKS FIXATION SACCADES] --> S[EVENTNAME] [EYE] [TIMESTAMP]
# End of EVENTS --> E[EVENT] [EYE] [TIMESTAMP_START]\t [TIMESTAMP_END]\t [TIME OF EVENT]\t [X-Coords start]\t [Y-Coords start]\t [X_Coords end]\t [Y-Coords end]\t [?]\t [?]
# Trial messages --> MSG timestamp\t TRIAL [TRIALNUMBER]
try:
with open(directory) as f:
csv_reader = csv.reader(f, delimiter ='\t')
for i, row in enumerate (csv_reader):
if any ('RATE' in item for item in row):
sample_rate_info = row
if any('SYNCTIME' in item for item in row): # only start reading after this message
start_reading = True
elif any('SFIX' in item for item in row): pass
#fix_timestamps[0].append (row)
elif any('EFIX' in item for item in row):
fix_timestamps.append ([row[0].split(' ')[4],row[1]])
#fix_timestamps[1].append (row)
elif any('SSACC' in item for item in row):
#sac_timestamps[0].append (row)
in_saccade = True
elif any('ESACC' in item for item in row):
sac_timestamps.append ([row[0].split(' ')[3],row[1]])
in_saccade = False
elif any('SBLINK' in item for item in row): # stop reading here because the blinks contain NaN
# blink_timestamps[0].append (row)
in_blink = True
elif any('EBLINK' in item for item in row): # start reading again. the blink ended
blink_timestamps.append ([row[0].split(' ')[2],row[1]])
in_blink = False
elif any('TRIAL' in item for item in row):
# the first element is 'MSG', we don't need it, then we split the second element to seperate the timestamp and only keep it as an integer
trials.append (int(row[1].split(' ')[0]))
elif start_reading and not in_blink:
eye_data.append(row)
if in_saccade:
sac_data.append(row)
else:
fix_data.append(row)
# drop the last data point, because it is the 'END' message
eye_data.pop(-1)
sac_data.pop(-1)
fix_data.pop(-1)
# convert every item in list into a float, substract the start of the first trial to set the start of the first video to t0=0
# then devide by 1000 to convert from milliseconds to seconds
for row in eye_data:
for i, item in enumerate (row):
row[i] = float (item)
for row in fix_data:
for i, item in enumerate (row):
row[i] = float (item)
for row in sac_data:
for i, item in enumerate (row):
row[i] = float (item)
for row in fix_timestamps:
for i, item in enumerate (row):
row [i] = (float(item)-trials[0])/1000
for row in sac_timestamps:
for i, item in enumerate (row):
row [i] = (float(item)-trials[0])/1000
for row in blink_timestamps:
for i, item in enumerate (row):
row [i] = (float(item)-trials[0])/1000
sample_rate = float (sample_rate_info[4])
# convert into pandas fix_data Frames for a better overview
eye_data = pd.DataFrame(eye_data)
fix_data = pd.DataFrame(fix_data)
sac_data = pd.DataFrame(sac_data)
fix_timestamps = pd.DataFrame(fix_timestamps)
sac_timestamps = pd.DataFrame(sac_timestamps)
trials = np.array(trials)
blink_timestamps = pd.DataFrame(blink_timestamps)
# rename header for an even better overview
eye_data = eye_data.rename(columns=data_header)
fix_data = fix_data.rename(columns=data_header)
sac_data = sac_data.rename(columns=data_header)
fix_timestamps = fix_timestamps.rename(columns=event_header)
sac_timestamps = sac_timestamps.rename(columns=event_header)
blink_timestamps = blink_timestamps.rename(columns=event_header)
# substract the first timestamp of trials to set the start of the first video to t0=0
eye_data.TimeStamp -= trials[0]
fix_data.TimeStamp -= trials[0]
sac_data.TimeStamp -= trials[0]
trials -= trials[0]
trials = trials /1000 # does not work with trials/=1000
# devide TimeStamp to get time in seconds
eye_data.TimeStamp /=1000
fix_data.TimeStamp /=1000
sac_data.TimeStamp /=1000
return eye_data, fix_data, sac_data, fix_timestamps, sac_timestamps, blink_timestamps, trials, sample_rate
except:
print ('Could not read ' + str(directory) + ' properly!!! Returned empty data')
return eye_data, fix_data, sac_data, fix_timestamps, sac_timestamps, blink_timestamps, trials, sample_rate
Hope it helps you guys. Some parts of the code you may need to change, like the index where to split the strings to get the crutial information about event on/offsets. Or you don't want to convert your timestamps into seconds or do not want to set the onset of your first trial to 0. That is up to you.
Additionally in my data we sent a message to know when we started measuring ('SYNCTIME') and I had only ONE condition in my experiment, so there is only one 'TRIAL' message
Cheers

Search the nth number of string in side the another list in python

add name, where is a string denoting a contact name. This must store as a new contact in the application.
find partial, where is a string denoting a partial name to search the application for. It must count the number of contacts starting with and print the count on a new line.
Given sequential add and find operations, perform each operation in order.
Input:
4
add hack
add hackerrank
find hac
find hak
Sample Output
2
0
We perform the following sequence of operations:
1.Add a contact named hack.
2.Add a contact named hackerrank.
3.Find and print the number of contact names beginning with hac.
There are currently two contact names in the application
and both of them start with hac, so we print 2 on a new line.
4.Find and print the number of contact names beginning with hak.
There are currently two contact names in the application
but neither of them start with hak, so we print 0 on a new line.
i solved it but it is taking long time for large number of string. my code is
addlist =[]
findlist=[]
n = int(input().strip())
for a0 in range(n):
op, contact = input().strip().split(' ')
if(op=='add'):
addlist.append(contact)
else:
findlist.append(contact)
for item in findlist:
count=0
count=[count+1 for item2 in addlist if item in item2 if item==item2[0:len(item)]]
print(sum(count))
is there any other way to avoid the long time to computation.
As far as optimizing goes I broke your code apart a bit for readability and removed a redundant if statement. I'm not sure if its possible to optimize any further.
addlist =[]
findlist=[]
n = int(input().strip())
for a0 in range(n):
op, contact = input().strip().split(' ')
if(op=='add'):
addlist.append(contact)
else:
findlist.append(contact)
for item in findlist:
count = 0
for item2 in addlist:
if item == item2[0:len(item)]:
count += 1
print(count)
I tested 10562 entries at once and it processed instantly so if it lags for you it can be blamed on your processor

String to dictionary word count and display

I have a homework question which asks:
Write a function print_word_counts(filename) that takes the name of a
file as a parameter and prints an alphabetically ordered list of all
words in the document converted to lower case plus their occurrence
counts (this is how many times each word appears in the file).
I am able to get an out of order set of each word with it's occurrence; however when I sort it and make it so each word is on a new line the count disappears.
import re
def print_word_counts(filename):
input_file = open(filename, 'r')
source_string = input_file.read().lower()
input_file.close()
words = re.findall('[a-zA-Z]+', source_string)
counts = {}
for word in words:
counts[word] = counts.get(word, 0) + 1
sorted_count = sorted(counts)
print("\n".join(sorted_count))
When I run this code I get:
a
aborigines
absence
absolutely
accept
after
and so on.
What I need is:
a: 4
aborigines: 1
absence: 1
absolutely: 1
accept: 1
after: 1
I'm not sure how to sort it and keep the values.
It's a homework question, so I can't give you the full answer, but here's enough to get you started. Your mistake is in this line
sorted_count = sorted(counts)
Firstly, you cant sort a dictionary by nature. Secondly, what this does is take the keys of the dictionary, sorts them, and returns a list.
You can just print the value of counts, or, if you really need them in sorted order, consider changing the dictionary items into a list, then sorting them.
lst = list(count.items())
#sort and return lst

Generators for processing large result sets

I am retrieving information from a sqlite DB that gives me back around 20 million rows that I need to process. This information is then transformed into a dict of lists which I need to use. I am trying to use generators wherever possible.
Can someone please take a look at this code and suggest optimization please? I am either getting a “Killed” message or it takes a really long time to run. The SQL result set part is working fine. I tested the generator code in the Python interpreter and it doesn’t have any problems. I am guessing the problem is with the dict generation.
EDIT/UPDATE FOR CLARITY:
I have 20 million rows in my result set from my sqlite DB. Each row is of the form:
(2786972, 486255.0, 4125992.0, 'AACAGA', '2005’)
I now need to create a dict that is keyed with the fourth element ‘AACAGA’ of the row. The value that the dict will hold is the third element, but it has to hold the values for all the occurences in the result set. So, in our case here, ‘AACAGA’ will hold a list containing multiple values from the sql result set. The problem here is to find tandem repeats in a genome sequence. A tandem repeat is a genome read (‘AACAGA’) that is repeated atleast three times in succession. For me to calculate this, I need all the values in the third index as a list keyed by the genome read, in our case ‘AACAGA’. Once I have the list, I can subtract successive values in the list to see if there are three consecutive matches to the length of the read. This is what I aim to accomplish with the dictionary and lists as values.
#!/usr/bin/python3.3
import sqlite3 as sql
sequence_dict = {}
tandem_repeat = {}
def dict_generator(large_dict):
dkeys = large_dict.keys()
for k in dkeys:
yield(k, large_dict[k])
def create_result_generator():
conn = sql.connect('sequences_mt_test.sqlite', timeout=20)
c = conn.cursor()
try:
conn.row_factory = sql.Row
sql_string = "select * from sequence_info where kmer_length > 2"
c.execute(sql_string)
except sql.Error as error:
print("Error retrieving information from the database : ", error.args[0])
result_set = c.fetchall()
if result_set:
conn.close()
return(row for row in result_set)
def find_longest_tandem_repeat():
sortList = []
for entry in create_result_generator():
sequence_dict.setdefault(entry[3], []).append(entry[2])
for key,value in dict_generator(sequence_dict):
sortList = sorted(value)
for i in range (0, (len(sortList)-1)):
if((sortList[i+1]-sortList[i]) == (sortList[i+2]-sortList[i+1])
== (sortList[i+3]-sortList[i+2]) == (len(key))):
tandem_repeat[key] = True
break
print(max(k for k, v in tandem_repeat.items() if v))
if __name__ == "__main__":
find_longest_tandem_repeat()
I got some help with this on codereview as #hivert suggested. Thanks. This is much better solved in SQL rather than just code. I was new to SQL and hence could not write complex queries. Someone helped me out with that.
SELECT *
FROM sequence_info AS middle
JOIN sequence_info AS preceding
ON preceding.sequence_info = middle.sequence_info
AND preceding.sequence_offset = middle.sequence_offset -
length(middle.sequence_info)
JOIN sequence_info AS following
ON following.sequence_info = middle.sequence_info
AND following.sequence_offset = middle.sequence_offset +
length(middle.sequence_info)
WHERE middle.kmer_length > 2
ORDER BY length(middle.sequence_info) DESC, middle.sequence_info,
middle.sequence_offset;
Hope this helps someone with around the same idea. Here is a link to the thread on codereview.stackexchange.com

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