I do have a large dataset (around 8 million rows x 25 columns) in Pandas and I am struggling to find a way to compute weighted average on this dataframe which in turn creates another data frame.
Here is how my dataset looks like (very simplified version of it):
prec temp
location_id hours
135 1 12.0 4.0
2 14.0 4.1
3 14.3 3.5
4 15.0 4.5
5 15.0 4.2
6 15.0 4.7
7 15.5 5.1
136 1 12.0 4.0
2 14.0 4.1
3 14.3 3.5
4 15.0 4.5
5 15.0 4.2
6 15.0 4.7
7 15.5 5.1
I have a multi-index on [location_id, hours]. I have around 60k locations and 140 hours for each location (making up the 8 million rows).
The rest of the data is numeric (float) or categorical. I have only included 2 columns here, normally there are around 20 columns.
What I am willing to do is to create a new data frame that is basically a weighted average of this data frame. The requirements indicate that 12 of these location_ids should be averaged out by a specified weight to form the combined_location_id values.
For example, location_ids 1,3,5,7,9,11,13,15,17,19,21,23 with their appropriate weights (separate data coming in from another data frame) should be weighted averaged to from the combined_location_id CL_1's data.
That is a lot of data to handle and I wasn't able to find a completely Pandas way of solving it. Therefore, I went with a for loop approach. It is extremely slow and I am sure this is not the right way to do it:
def __weighted(self, ds, weights):
return np.average(ds, weights=weights)
f = {'hours': 'first', 'location_id': 'first',
'temp': lambda x: self.__weighted(x, weights), 'prec': lambda x: self.__weighted(x, weights)}
data_frames = []
for combined_location in all_combined_locations:
mapped_location_ids = combined_location.location_ids
weights = combined_location.weights_of_location_ids
data_for_this_combined_location = pd.concat(df_data.loc[df_data.index.get_level_values(0) == location_id] for location_id in mapped_location_ids)
data_grouped_by_distance = data_for_this_combined_location.groupby("hours", as_index=False)
data_grouped_by_distance = data_grouped_by_distance.agg(f)
data_frames.append(data_grouped_by_distance)
df_combined_location_data = pd.concat(data_frames)
df_combined_location_data.set_index(['location_id', 'hours'], inplace=True)
This works well functionally, however the performance and the memory consumption is horrible. It is taking over 2 hours on my dataset and that is currently not acceptable. The existence of the for loop is an indicator that this could be handled better.
Is there a better/faster way to implement this?
From what I saw you can reduce one for loop with mapped_location_ids
data_for_this_combined_location = df_data.loc[df_data.index.get_level_values(0).isin(mapped_location_ids)]
Related
I'm struggling to solve this problem. I'm creating a data frame that is generated by data that can vary from one day to another but I need to save the first version and block new updates.
This is the code:
# Create data frame for the ideal burndown line
df_ideal_burndown = pd.DataFrame(columns=['dates', 'ideal_trend'])
df_ideal_burndown['dates'] = range_sprint
#### Dates preparation
df_ideal_burndown['dates'] = pd.to_datetime(df_ideal_burndown['dates'], dayfirst=True)
df_ideal_burndown['dates'] = df_ideal_burndown['dates'].dt.strftime('%Y-%m-%d')
# Define the sprint lenght
days_sprint = int(len(range_sprint)) - int(cont_nonworking)
# Get how many items are in the current sprint
commited = len(df_current_sprint)
# Define the ideal number of items should be delivered by day
ideal_burn = round(commited/days_sprint,1)
# Create a list of remaining items to be delivered by day
burndown = [commited - ideal_burn]
# Day of the sprint -> starts with 2, since the first day is already in the list above
sprint_day = 2
# Iterate to create the ideal trend line in numbers
for i in range(1, len(df_ideal_burndown), 1):
burndown.append(round((commited - (ideal_burn * sprint_day)),1))
sprint_day += 1
# Add the ideal burndown to the column
df_ideal_burndown['ideal_trend'] = burndown
df_ideal_burndown
This is the output:
dates ideal_trend
0 2022-03-14 18.7
1 2022-03-15 17.4
2 2022-03-16 16.1
3 2022-03-17 14.8
4 2022-03-18 13.5
5 2022-03-21 12.2
6 2022-03-22 10.9
7 2022-03-23 9.6
8 2022-03-24 8.3
9 2022-03-25 7.0
10 2022-03-28 5.7
11 2022-03-29 4.4
12 2022-03-30 3.1
13 2022-03-31 1.8
14 2022-04-01 0.5
My main problem is related to commited = len(df_current_sprint), since the df_current_sprint is (and needs to be) used by other parts of my code.
Basically, even if the API returns new data that should be stored in the df_current_sprint I should use the version I'd just created.
I am pretty new to Python and I do not know if there is a way to store and, let's say, cache this information until I need to use fresh new data.
I appreciate your support, clues, and guidance.
Marcelo
i try to calculate the position of an object based on a timestamp. For this I have two dataframes in pandas. One for the measurement data and one for the position. All the movement is a straightforward acceleration.
Dataframe 1 contains the measurement data:
ms force ... ... ...
1 5 20
2 10 20
3 15 25
4 20 30
5 25 20
..... (~ 6000 lines)
Dataframe 2 contains "positioning data"
ms speed (m/s)
1 0 0.66
2 4500 0.66
3 8000 1.3
4 16000 3.0
5 20000 3.0
.....(~300 lines)
Now I want to calculate the position of the first dataframe with the data from secound dataframe
In Excel I solved the problem by using an array formular but now I have to use Python/Pandas and I cant find a way how to select the correct row from dataframe 2.
My idea is to make something like this: if
In the end I want to display a graph "force <-> way" and not "force <-> time"
Thank you in andvance
==========================================================================
Update:
In the meantime I could almost solve my issue. Now my Data look like this:
Dataframe 2 (Speed Data):
pos v a t t-end t-start
0 -3.000 0.666667 0.000000 4.500000 4.500000 0.000000
1 0.000 0.666667 0.187037 0.071287 4.571287 4.500000
2 0.048 0.680000 0.650794 0.010244 4.581531 4.571287
3 0.055 0.686667 0.205432 0.064904 4.646435 4.581531
...
15 0.055 0.686667 0.5 0.064904 23.0 20.0
...
28 0.055 0.686667 0.6 0.064904 35.0 34.0
...
30 0.055 0.686667 0.9 0.064904 44.0 39.0
And Dataframe 1 (time based measurement):
Fx Fy Fz abs_t expected output ('a' from DF1)
0 -13.9 170.3 45.0 0.005 0.000000
1 -14.1 151.6 38.2 0.010 0.000000
...
200 -14.1 131.4 30.4 20.015 0.5
...
300 -14.3 111.9 21.1 34.01 0.6
...
400 -14.5 95.6 13.2 40.025
So i want to check the time(abs_t) from DF1 and search for the corract 'a' in DF2
So somthing like this (pseudo code):
if (DF1['t_abs'] between (DF2['t-start'], DF2['t-end']):
DF1['a'] = DF2['a']
I could make two for loops but it looks like the wrong way and is very very slow.
I hope you understand my problem; to provide a running sample is very hard.
In Excel I did like this:
I found a very slow solution but atleast its working :(
df1['a'] = 0
for index, row in df2.iterrows():
start = row['t-start']
end = row ['t-end']
a = row ['a']
df1.loc[(df1['tabs']>start)&(df1['tabs']<end), 'a'] = a
I have a pandas dataframe containing 16 columns, of which 14 represent variables where i perform a looped Anova test using statsmodels. My dataframe looks something like this (simplified):
ID Cycle_duration Average_support_phase Average_swing_phase Label
1 23.1 34.3 47.2 1
2 27.3 38.4 49.5 1
3 25.8 31.1 45.7 1
4 24.5 35.6 41.9 1
...
So far this is what i'm doing:
import pandas as pd
import statsmodels.api as sm
from statsmodels.formula.api import ols
df = pd.read_csv('features_total.csv')
for variable in df.columns:
model = ols('{} ~ Label'.format(variable), data=df).fit()
anova_table = sm.stats.anova_lm(model, typ=2)
print(anova_table)
Which yields:
sum_sq df F PR(>F)
Label 0.124927 2.0 2.561424 0.084312
Residual 1.731424 71.0 NaN NaN
sum_sq df F PR(>F)
Label 62.626057 2.0 4.969491 0.009552
Residual 447.374788 71.0 NaN NaN
sum_sq df F PR(>F)
Label 62.626057 2.0 4.969491 0.009552
Residual 447.374788 71.0 NaN NaN
I'm getting an individual table print for each variable where the Anova is performed. Basically what i want is to print one single table with the summarized results, or something like this:
sum_sq df F PR(>F)
Cycle_duration 0.1249270 2.0 2.561424 0.084312
Residual 1.7314240 71.0 NaN NaN
Average_support_phase 62.626057 2.0 4.969491 0.009552
Residual 447.374788 71.0 NaN NaN
Average_swing_phase 62.626057 2.0 4.969491 0.009552
Residual 447.374788 71.0 NaN NaN
I can already see a problem because this method always outputs the 'Label' nomenclature before the actual values, and not the variable name in question (like i've shown above, i would like to have the variable name above each 'residual'). Is this even possible with the statsmodels approach?
I'm fairly new to python and excuse me if this has nothing to do with statsmodels - in that case, please do elucidate me on what i should be trying.
You can collect the tables and concatenate them at the end of your loop. This method will create a hierarchical index, but I think that makes it a bit more clear. Something like this:
keys = []
tables = []
for variable in df.columns:
model = ols('{} ~ Label'.format(variable), data=df).fit()
anova_table = sm.stats.anova_lm(model, typ=2)
keys.append(variable)
tables.append(anova_table)
df_anova = pd.concat(tables, keys=keys, axis=0)
Somewhat related, I would also suggest correcting for multiple comparisons. This is more a statistical suggestion than a coding suggestion, but considering you are performing numerous statistical tests, it would make sense to account for the probability that one of the test would result in a false positive.
This question already has answers here:
Pandas: Difference to previous value
(2 answers)
Closed 3 years ago.
I trying to get the avarage, max and min time difference between value occurrences in a csv file.
The contains a multiple columns and rows.
I am currently working in python and trying to use pandas to solve my problem.
I have managed to break down the csv file to the column i want to get the time difference from and the time column.
Where the "payload" column "value occurrences" happens.
looking like:
time | payload
12.1 2368
13.8 2508
I have also tried to get the time in a array when the value occurrences happens and tried to step through the array but failed bad. I felt like there was a easier way to do it.
def average_time(avg_file):
avg_read = pd.read_csv(avg_file, skiprows=2, names=new_col_names, usecols=[2, 3], na_filter=False, skip_blank_lines=True)
test=[]
i=0
for row in avg_read.payload:
if row != None:
test[i]=avg_read.time
i+=1
if len[test] > 2:
average=test[1]-test[0]
i=0
test=[]
return average
The csv-file currently look like:
time | payload
12.1 2250
12.5 2305
12.9 (blank)
13.1 (blank)
13.5 2309
14.6 2350
14.9 2680
15.0 (blank)
I want to get the time diffenrence between the values in the payload columen. example time between
2250 and 2305 --> 12.5-12.1 = 0.4 sec
and the get the difference between
2305 and 2309 --> 13.5-12.5 = 1 s
Skipping the blank numbers
To later on get the maximum, minimun and average difference.
First use dropna then use Series.diff
DataFrame used:
print(df)
time payload
0 12.1 2250.0
1 12.5 2305.0
2 12.9 NaN
3 13.1 NaN
4 13.5 2309.0
5 14.6 2350.0
6 14.9 2680.0
7 15.0 NaN
df.dropna().time.diff()
0 NaN
1 0.4
4 1.0
5 1.1
6 0.3
Name: time, dtype: float64
Note I assumed your (blank) values are NaN, else use the following before running my code:
df.replace('(blank)', np.NaN, inplace=True, axis=1)
# Or if they are whitespaces
df.replace('', np.NaN, inplace=True, axis=1)
I have a pandas dataframe that has raw heart rate data with the index of time (in seconds).
I am trying to bin the data so that I can have the average of a user define window (e.g. 10s) - not a rolling average, just an average of 10s, then the 10s following, etc.
import pandas as pd
hr_raw = pd.read_csv('hr_data.csv', index_col='time')
print(hr_raw)
heart_rate
time
0.6 164.0
1.0 182.0
1.3 164.0
1.6 150.0
2.0 152.0
2.4 141.0
2.9 163.0
3.2 141.0
3.7 124.0
4.2 116.0
4.7 126.0
5.1 116.0
5.7 107.0
Using the example data above, I would like to be able to set a user defined window size (let's use 2 seconds) and produce a new dataframe that has index of 2sec increments and averages the 'heart_rate' values if the time falls into that window (and should continue to the end of the dataframe).
For example:
heart_rate
time
2.0 162.40
4.0 142.25
6.0 116.25
I can only seem to find methods to bin the data based on a predetermined number of bins (e.g. making a histogram) and this only returns the count/frequency.
thanks.
A groupby should do it.
df.groupby((df.index // 2 + 1) * 2).mean()
heart_rate
time
2.0 165.00
4.0 144.20
6.0 116.25
Note that the reason for the slight difference between our answers is that the upper bound is excluded. That means, a reading taken at 2.0s will be considered for the 4.0s time interval. This is how it is usually done, a similar solution with the TimeGrouper will yield the same result.
Like coldspeed pointed out, 2s will be considered in 4s, however, if you need it in 2x bucket, you can
In [1038]: df.groupby(np.ceil(df.index/2)*2).mean()
Out[1038]:
heart_rate
time
2.0 162.40
4.0 142.25
6.0 116.25