I am trying to create a new column, in which e.g. the time 14:02 should be saved as 14.0, whereas 14:16 should be 14.5. This would equal half-hour units. Of course 15min units should also be creatable and so on. This is my approach for full hours, but I need a higher resolution.
df["Time"] = df.StartDateTime.apply(lambda x: x.hour)
So long as the units evenly divide an hour you can round with that frequency and then divide by an hour.
import pandas as pd
df = pd.DataFrame({'Time': pd.timedelta_range('14:00:00', freq='4min', periods=10)})
for freq in ['30min', '15min', '20min', '10min']:
df[freq] = df['Time'].dt.round(freq)/pd.Timedelta('1H')
Time 30min 15min 20min 10min
0 14:00:00 14.0 14.00 14.000000 14.000000
1 14:04:00 14.0 14.00 14.000000 14.000000
2 14:08:00 14.0 14.25 14.000000 14.166667
3 14:12:00 14.0 14.25 14.333333 14.166667
4 14:16:00 14.5 14.25 14.333333 14.333333
5 14:20:00 14.5 14.25 14.333333 14.333333
6 14:24:00 14.5 14.50 14.333333 14.333333
7 14:28:00 14.5 14.50 14.333333 14.500000
8 14:32:00 14.5 14.50 14.666667 14.500000
9 14:36:00 14.5 14.50 14.666667 14.666667
If you start from a datetime64[ns] column you can isolate the time by subtracting off the normalized date. For example:
df = pd.DataFrame({'Time': pd.date_range('2010-01-01 14:00:00', freq='4min', periods=5)})
df['Time_only'] = df['Time'] - df['Time'].dt.normalize()
# Time Time_only
#0 2010-01-01 14:00:00 14:00:00
#1 2010-01-01 14:04:00 14:04:00
#2 2010-01-01 14:08:00 14:08:00
#3 2010-01-01 14:12:00 14:12:00
#4 2010-01-01 14:16:00 14:16:00
print(df.dtypes)
#Time datetime64[ns]
#Time_only timedelta64[ns]
#dtype: object
Related
I am encountering an errors each time i attempt to compute the difference in readings for a meter in my dataset. The dataset structure is this.
id paymenttermid houseid houseid-meterid quantity month year cleaned_quantity
Datetime
2019-02-01 255 water 215 215M201 23.0 2 2019 23.0
2019-02-01 286 water 193 193M181 24.0 2 2019 24.0
2019-02-01 322 water 172 172M162 22.0 2 2019 22.0
2019-02-01 323 water 176 176M166 61.0 2 2019 61.0
2019-02-01 332 water 158 158M148 15.0 2 2019 15.0
I am attempting to generate a new column called consumption that computes the difference in quantities consumed for each house(identified by houseid-meterid) after every month of the year.
The code i am using to implement this is:
water_df["consumption"] = water_df.groupby(["year", "month", "houseid-meterid"])["cleaned_quantity"].diff(-1)
After executing this code, the consumption column is filled with NaN values. How can I correctly implement this logic.
The end result looks like this:
id paymenttermid houseid houseid-meterid quantity month year cleaned_quantity consumption
Datetime
2019-02-01 255 water 215 215M201 23.0 2 2019 23.0 NaN
2019-02-01 286 water 193 193M181 24.0 2 2019 24.0 NaN
2019-02-01 322 water 172 172M162 22.0 2 2019 22.0 NaN
2019-02-01 323 water 176 176M166 61.0 2 2019 61.0 NaN
2019-02-01 332 water 158 158M148 15.0 2 2019 15.0 NaN
Many thank in advance.
I have attempted to use
water_df["consumption"] = water_df.groupby(["year", "month", "houseid-meterid"])["cleaned_quantity"].diff(-1)
and
water_df["consumption"] = water_df.groupby(["year", "month", "houseid-meterid"])["cleaned_quantity"].diff(0)
and
water_df["consumption"] = water_df.groupby(["year", "month", "houseid-meterid"])["cleaned_quantity"].diff()
all this commands result in the same behaviour as stated above.
Expected output should be:
Datetime houseid-meterid cleaned_quantity consumption
2019-02-01 215M201 23.0 20
2019-03-02 215M201 43.0 9
2019-04-01 215M201 52.0 12
2019-05-01 215M201 64.0 36
2019-06-01 215M201 100.0 20
what steps should i take?
Sort values by Datetime (if needed) then group by houseid-meterid before compute the diff for cleaned_quantity values then shift row to align with the right data:
df['consumption'] = (df.sort_values('Datetime')
.groupby('houseid-meterid')['cleaned_quantity']
.transform(lambda x: x.diff().shift(-1)))
print(df)
# Output
Datetime houseid-meterid cleaned_quantity consumption
0 2019-02-01 215M201 23.0 20.0
1 2019-03-02 215M201 43.0 9.0
2 2019-04-01 215M201 52.0 12.0
3 2019-05-01 215M201 64.0 36.0
4 2019-06-01 215M201 100.0 NaN
I would like to resample a DataFrame with frequences of 10D but cutting the last decade always at the end of the month.
ES:
print(df)
data
index
2010-01-01 145.08
2010-01-02 143.69
2010-01-03 101.06
2010-01-04 57.63
2010-01-05 65.46
...
2010-02-24 48.06
2010-02-25 87.41
2010-02-26 71.97
2010-02-27 73.1
2010-02-28 41.43
Apply something like df.resample('10DM').mean()
data
index
2010-01-10 97.33
2010-01-20 58.58
2010-01-31 41.43
2010-02-10 35.17
2010-02-20 32.44
2010-02-28 55.44
note that the 1st and 2nd decades are normal 10D resample, but the 3rd can be 8-9-10-11 days based on month and year.
Thanks in advance.
Sample data (easy to check):
# df = pd.DataFrame({"value": np.arange(1, len(dti)+1)}, index=dti)
>>> df
value
2010-01-01 1
2010-01-02 2
2010-01-03 3
2010-01-04 4
2010-01-05 5
...
2010-02-24 55
2010-02-25 56
2010-02-26 57
2010-02-27 58
2010-02-28 59
You need to create groups by (days, month, year):
grp = df.groupby([pd.cut(df.index.day, [0, 10, 20, 31]),
pd.Grouper(freq='M'),
pd.Grouper(freq='Y')])
Now you can compute the mean for each group:
out = grp['value'].apply(lambda x: (x.index.max(), x.mean())).apply(pd.Series) \
.reset_index(drop=True).rename(columns={0:'date', 1:'value'}) \
.set_index('date').sort_index()
Output result:
>>> out
value
date
2010-01-10 5.5
2010-01-20 15.5
2010-01-31 26.0
2010-02-10 36.5
2010-02-20 46.5
2010-02-28 55.5
I have df1:
Date
Symbol
Time
Quantity
Price
2020-09-04
AAPL
09:54:48
11.0
115.97
2020-09-16
AAPL
09:30:02
-11.0
115.33
2020-02-24
AMBA
09:30:02
22.0
64.24
2020-02-25
AMBA
14:01:28
-22.0
62.64
2020-07-14
AMGN
09:30:01
5.0
243.90
...
...
...
...
...
2020-12-08
YUMC
09:30:00
-22.0
56.89
2020-11-18
Z
14:20:01
12.0
100.68
2020-11-20
Z
09:30:01
-12.0
109.25
2020-09-04
ZS
09:45:24
9.0
135.94
2020-09-14
ZS
09:38:23
-9.0
126.41
and df2:
Date
USD
2
2020-02-01
22.702
3
2020-03-01
22.753
4
2020-06-01
22.601
5
2020-07-01
22.626
6
2020-08-01
22.739
..
...
...
248
2020-12-23
21.681
249
2020-12-28
21.482
250
2020-12-29
21.462
251
2020-12-30
21.372
252
2020-12-31
21.387
I want to add a new column "USD" from df2 by date in df1.
Trying
new_df = (dane5.reset_index()
.merge(kurz2,how='outer')
.fillna(0)
.set_index('Date'))
new_df.sort_index(inplace=True)
new_df= new_df[new_df['Symbol'] != 0]
print(new_df.head(50))
But I return zero value some rows:
Date
Symbol
Time
Quantity
Price
USD
2020-01-02
GL
10:31:14
13.0
104.550000
0.000
2020-01-02
ATEC
13:35:04
211.0
6.860000
0.000
2020-01-03
IOVA
14:02:32
56.0
25.790000
0.000
2020-01-03
TGNA
09:30:00
90.0
16.080000
0.000
2020-01-03
SCS
09:30:01
-70.0
20.100000
0.000
2020-01-03
SKX
09:30:09
34.0
41.940000
0.000
2020-01-06
IOVA
09:45:19
-56.0
24.490000
24.163
2020-01-06
GL
09:30:02
-13.0
103.430000
24.163
2020-01-06
SKX
15:55:15
-34.0
43.900000
24.163
2020-01-07
TGNA
15:55:16
-90.0
16.945000
23.810
2020-01-07
MRTX
09:46:18
-13.0
101.290000
23.810
2020-01-07
MRTX
09:34:10
13.0
109.430000
23.810
2020-01-08
ITCI
09:30:01
49.0
27.640000
0.000
Could you some help me please?
Sorry my bad English language.
I have two data frames that stores different types of medical information of patients. The common elements of both the data frames are the encounter ID (hadm_id), the time the information was recorded ((n|c)e_charttime).
One data frame (df_str) contains structured information such as vital signs and lab test values and values derived from these (such as change statistics over 24 hours). The other data frame (df_notes) contains a column with a clinical note recorded at a specified time for an encounter. Both these data frames contain multiple encounters, but the common element is the encounter ID (hadm_id).
Here are examples of the data frames for ONE encounter ID (hadm_id) with a subset of variables:
df_str
hadm_id ce_charttime hr resp magnesium hr_24hr_mean
0 196673 2108-03-05 15:34:00 95.0 12.0 NaN 95.000000
1 196673 2108-03-05 16:00:00 85.0 11.0 NaN 90.000000
2 196673 2108-03-05 16:16:00 85.0 11.0 1.8 88.333333
3 196673 2108-03-05 17:00:00 109.0 12.0 1.8 93.500000
4 196673 2108-03-05 18:00:00 97.0 12.0 1.8 94.200000
5 196673 2108-03-05 19:00:00 99.0 16.0 1.8 95.000000
6 196673 2108-03-05 20:00:00 98.0 13.0 1.8 95.428571
7 196673 2108-03-05 21:00:00 97.0 14.0 1.8 95.625000
8 196673 2108-03-05 22:00:00 101.0 12.0 1.8 96.222222
9 196673 2108-03-05 23:00:00 97.0 13.0 1.8 96.300000
10 196673 2108-03-06 00:00:00 93.0 13.0 1.8 96.000000
11 196673 2108-03-06 01:00:00 89.0 12.0 1.8 95.416667
12 196673 2108-03-06 02:00:00 88.0 10.0 1.8 94.846154
13 196673 2108-03-06 03:00:00 87.0 12.0 1.8 94.285714
14 196673 2108-03-06 04:00:00 97.0 19.0 1.8 94.466667
15 196673 2108-03-06 05:00:00 95.0 11.0 1.8 94.500000
16 196673 2108-03-06 05:43:00 95.0 11.0 2.0 94.529412
17 196673 2108-03-06 06:00:00 103.0 17.0 2.0 95.000000
18 196673 2108-03-06 07:00:00 101.0 12.0 2.0 95.315789
19 196673 2108-03-06 08:00:00 103.0 20.0 2.0 95.700000
20 196673 2108-03-06 09:00:00 84.0 11.0 2.0 95.142857
21 196673 2108-03-06 10:00:00 89.0 11.0 2.0 94.863636
22 196673 2108-03-06 11:00:00 91.0 14.0 2.0 94.695652
23 196673 2108-03-06 12:00:00 85.0 10.0 2.0 94.291667
24 196673 2108-03-06 13:00:00 98.0 14.0 2.0 94.440000
25 196673 2108-03-06 14:00:00 100.0 18.0 2.0 94.653846
26 196673 2108-03-06 15:00:00 95.0 12.0 2.0 94.666667
27 196673 2108-03-06 16:00:00 96.0 20.0 2.0 95.076923
28 196673 2108-03-06 17:00:00 106.0 21.0 2.0 95.360000
df_notes
hadm_id ne_charttime note
0 196673 2108-03-05 16:54:00 Nursing\nNursing Progress Note\nPt is a 43 yo ...
1 196673 2108-03-05 17:54:00 Physician \nPhysician Resident Admission Note\...
2 196673 2108-03-05 18:09:00 Physician \nPhysician Resident Admission Note\...
3 196673 2108-03-06 06:11:00 Nursing\nNursing Progress Note\nPain control (...
4 196673 2108-03-06 08:06:00 Physician \nPhysician Resident Progress Note\n...
5 196673 2108-03-06 12:40:00 Nursing\nNursing Progress Note\nChief Complain...
6 196673 2108-03-06 13:01:00 Nursing\nNursing Progress Note\nPain control (...
7 196673 2108-03-06 17:09:00 Nursing\nNursing Transfer Note\nChief Complain...
8 196673 2108-03-06 17:12:00 Nursing\nNursing Transfer Note\nPain control (...
9 196673 2108-03-07 15:25:00 Radiology\nCHEST (PA & LAT)\n[**2108-3-7**] 3:...
10 196673 2108-03-07 18:34:00 Radiology\nCTA CHEST W&W/O C&RECONS, NON-CORON...
11 196673 2108-03-09 09:10:00 Radiology\nABDOMEN (SUPINE & ERECT)\n[**2108-3...
12 196673 2108-03-09 12:22:00 Radiology\nCT ABDOMEN W/CONTRAST\n[**2108-3-9*...
13 196673 2108-03-10 05:26:00 Radiology\nABDOMEN (SUPINE & ERECT)\n[**2108-3...
14 196673 2108-03-10 05:27:00 Radiology\nCHEST (PA & LAT)\n[**2108-3-10**] 5...
What I want to do is to combine both the data frames based on the time when that information was recorded. More specifically, for each row in df_notes, I want a corresponding row from df_str with ce_charttime <= ne_charttime.
As an example, the first row in df_notes has ne_charttime = 2108-03-05 16:54:00. There are three rows in df_str with record times less than this time: ce_charttime = 2108-03-05 15:34:00, ce_charttime = 2108-03-05 16:00:00, ce_charttime = 2108-03-05 16:16:00. The most recent of these is the row with ce_charttime = 2108-03-05 16:16:00. So in my resulting data frame, for ne_charttime = 2108-03-05 16:54:00, I will have hr = 85.0, resp = 11.0, magnesium = 1.8, hr_24hr_mean = 88.33.
Essentially, in this example the resulting data frame will look like this:
hadm_id ne_charttime note hr resp magnesium hr_24hr_mean
0 196673 2108-03-05 16:54:00 Nursing\nNursing Progress Note\nPt is a 43 yo ... 85.0 11.0 1.8 88.333333
1 196673 2108-03-05 17:54:00 Physician \nPhysician Resident Admission Note\... 109.0 12.0 1.8 93.500000
2 196673 2108-03-05 18:09:00 Physician \nPhysician Resident Admission Note\... 97.0 12.0 1.8 94.200000
3 196673 2108-03-06 06:11:00 Nursing\nNursing Progress Note\nPain control (... 103.0 17.0 2.0 95.000000
4 196673 2108-03-06 08:06:00 Physician \nPhysician Resident Progress Note\n... 103.0 20.0 2.0 95.700000
5 196673 2108-03-06 12:40:00 Nursing\nNursing Progress Note\nChief Complain... 85.0 10.0 2.0 94.291667
6 196673 2108-03-06 13:01:00 Nursing\nNursing Progress Note\nPain control (... 98.0 14.0 2.0 94.440000
7 196673 2108-03-06 17:09:00 Nursing\nNursing Transfer Note\nChief Complain... 106.0 21.0 2.0 95.360000
8 196673 2108-03-06 17:12:00 Nursing\nNursing Transfer Note\nPain control (... NaN NaN NaN NaN
9 196673 2108-03-07 15:25:00 Radiology\nCHEST (PA & LAT)\n[**2108-3-7**] 3:... NaN NaN NaN NaN
10 196673 2108-03-07 18:34:00 Radiology\nCTA CHEST W&W/O C&RECONS, NON-CORON... NaN NaN NaN NaN
11 196673 2108-03-09 09:10:00 Radiology\nABDOMEN (SUPINE & ERECT)\n[**2108-3... NaN NaN NaN NaN
12 196673 2108-03-09 12:22:00 Radiology\nCT ABDOMEN W/CONTRAST\n[**2108-3-9*... NaN NaN NaN NaN
13 196673 2108-03-10 05:26:00 Radiology\nABDOMEN (SUPINE & ERECT)\n[**2108-3... NaN NaN NaN NaN
14 196673 2108-03-10 05:27:00 Radiology\nCHEST (PA & LAT)\n[**2108-3-10**] 5... NaN NaN NaN NaN
The resulting data frame will be of the same length as df_notes. I have been able to come with a very inefficient piece of code using for loops and explicit indexing to get this result:
cols = list(df_str.columns[2:])
final_df = df_notes.copy()
for col in cols:
final_df[col] = np.nan
idx = 0
for i, note_row in final_df.iterrows():
ne = note_row['ne_charttime']
for j, str_row in df_str.iterrows():
ce = str_row['ce_charttime']
if ne < ce:
idx += 1
for col in cols:
final_df.iloc[i, final_df.columns.get_loc(col)] = df_str.iloc[j-1][col]
break
for col in cols:
final_df.iloc[idx, final_df.columns.get_loc(col)] = df_str.iloc[-1][col]
This piece of code is bad because it is very inefficient and while it may work for this example, in my example dataset, I have over 30 different columns of structured variables, and over 10,000 encounters.
EDIT-2:
#Stef has provided an excellent answer which seems to work and replace my elaborate loopy code with a single line (amazing). However, while that works for this particular example, I am running into problems when I apply it to a bigger subset which includes multiple encounters. For example, consider the following example:
df_str.shape, df_notes.shape
((217, 386), (35, 4))
df_notes[['hadm_id', 'ne_charttime']]
hadm_id ne_charttime
0 100104 2201-06-21 20:00:00
1 100104 2201-06-21 22:51:00
2 100104 2201-06-22 05:00:00
3 100104 2201-06-23 04:33:00
4 100104 2201-06-23 12:59:00
5 100104 2201-06-24 05:15:00
6 100372 2115-12-20 02:29:00
7 100372 2115-12-21 10:15:00
8 100372 2115-12-22 13:05:00
9 100372 2115-12-25 17:16:00
10 100372 2115-12-30 10:58:00
11 100372 2115-12-30 13:07:00
12 100372 2115-12-30 14:16:00
13 100372 2115-12-30 22:34:00
14 100372 2116-01-03 09:10:00
15 100372 2116-01-07 11:08:00
16 100975 2126-03-02 06:06:00
17 100975 2126-03-02 17:44:00
18 100975 2126-03-03 05:36:00
19 100975 2126-03-03 18:27:00
20 100975 2126-03-04 05:29:00
21 100975 2126-03-04 10:48:00
22 100975 2126-03-04 16:42:00
23 100975 2126-03-05 22:12:00
24 100975 2126-03-05 23:01:00
25 100975 2126-03-06 11:02:00
26 100975 2126-03-06 13:38:00
27 100975 2126-03-08 13:39:00
28 100975 2126-03-11 10:41:00
29 101511 2199-04-30 09:29:00
30 101511 2199-04-30 09:53:00
31 101511 2199-04-30 18:06:00
32 101511 2199-05-01 08:28:00
33 111073 2195-05-01 01:56:00
34 111073 2195-05-01 21:49:00
This example has 5 encounters. The dataframe is sorted by hadm_id and within each hadm_id, ne_charttime is sorted. However, the column ne_charttime by itself is NOT sorted as seen from row 0 ce_charttime=2201-06-21 20:00:00 and row 6 ne_charttime=2115-12-20 02:29:00. When I try to do a merge_asof, I get the following error:
ValueError: left keys must be sorted. Is this because of the fact that ne_charttime column is not sorted? If so, how do I rectify this while maintaining the integrity of the encounter ID group?
EDIT-1:
I was able to loop over the encounters as well:
cols = list(dev_str.columns[1:]) # get the cols to merge (everything except hadm_id)
final_dfs = []
grouped = dev_notes.groupby('hadm_id') # get groups of encounter ids
for name, group in grouped:
final_df = group.copy().reset_index(drop=True) # make a copy of notes for that encounter
for col in cols:
final_df[col] = np.nan # set the values to nan
idx = 0 # index to track the final row in the given encounter
for i, note_row in final_df.iterrows():
ne = note_row['ne_charttime']
sub = dev_str.loc[(dev_str['hadm_id'] == name)].reset_index(drop=True) # get the df corresponding to the ecounter
for j, str_row in sub.iterrows():
ce = str_row['ce_charttime']
if ne < ce: # if the variable charttime < note charttime
idx += 1
# grab the previous values for the variables and break
for col in cols:
final_df.iloc[i, final_df.columns.get_loc(col)] = sub.iloc[j-1][col]
break
# get the last value in the df for the variables
for col in cols:
final_df.iloc[idx, final_df.columns.get_loc(col)] = sub.iloc[-1][col]
final_dfs.append(final_df) # append the df to the list
# cat the list to get final df and reset index
final_df = pd.concat(final_dfs)
final_df.reset_index(inplace=True, drop=True)
Again this very inefficient but does the job.
Is there a better way to achieve what I want? Any help is appreciated.
Thanks.
You can use merge_asof (both dataframes must be sorted by the columns you're merging them on, which is already the case in your example):
final_df = pd.merge_asof(df_notes, df_str, left_on='ne_charttime', right_on='ce_charttime', by='hadm_id')
Result:
hadm_id ne_charttime note ce_charttime hr resp magnesium hr_24hr_mean
0 196673 2108-03-05 16:54:00 Nursing\nNursing Progress Note\nPt is a 43 yo ... 2108-03-05 16:16:00 85.0 11.0 1.8 88.333333
1 196673 2108-03-05 17:54:00 Physician \nPhysician Resident Admission Note\... 2108-03-05 17:00:00 109.0 12.0 1.8 93.500000
2 196673 2108-03-05 18:09:00 Physician \nPhysician Resident Admission Note\... 2108-03-05 18:00:00 97.0 12.0 1.8 94.200000
3 196673 2108-03-06 06:11:00 Nursing\nNursing Progress Note\nPain control (... 2108-03-06 06:00:00 103.0 17.0 2.0 95.000000
4 196673 2108-03-06 08:06:00 Physician \nPhysician Resident Progress Note\n... 2108-03-06 08:00:00 103.0 20.0 2.0 95.700000
5 196673 2108-03-06 12:40:00 Nursing\nNursing Progress Note\nChief Complain... 2108-03-06 12:00:00 85.0 10.0 2.0 94.291667
6 196673 2108-03-06 13:01:00 Nursing\nNursing Progress Note\nPain control (... 2108-03-06 13:00:00 98.0 14.0 2.0 94.440000
7 196673 2108-03-06 17:09:00 Nursing\nNursing Transfer Note\nChief Complain... 2108-03-06 17:00:00 106.0 21.0 2.0 95.360000
8 196673 2108-03-06 17:12:00 Nursing\nNursing Transfer Note\nPain control (... 2108-03-06 17:00:00 106.0 21.0 2.0 95.360000
9 196673 2108-03-07 15:25:00 Radiology\nCHEST (PA & LAT)\n[**2108-3-7**] 3:... 2108-03-06 17:00:00 106.0 21.0 2.0 95.360000
10 196673 2108-03-07 18:34:00 Radiology\nCTA CHEST W&W/O C&RECONS, NON-CORON... 2108-03-06 17:00:00 106.0 21.0 2.0 95.360000
11 196673 2108-03-09 09:10:00 Radiology\nABDOMEN (SUPINE & ERECT)\n[**2108-3... 2108-03-06 17:00:00 106.0 21.0 2.0 95.360000
12 196673 2108-03-09 12:22:00 Radiology\nCT ABDOMEN W/CONTRAST\n[**2108-3-9*... 2108-03-06 17:00:00 106.0 21.0 2.0 95.360000
13 196673 2108-03-10 05:26:00 Radiology\nABDOMEN (SUPINE & ERECT)\n[**2108-3... 2108-03-06 17:00:00 106.0 21.0 2.0 95.360000
14 196673 2108-03-10 05:27:00 Radiology\nCHEST (PA & LAT)\n[**2108-3-10**] 5... 2108-03-06 17:00:00 106.0 21.0 2.0 95.360000
PS: This gives you the correct result for all rows. There's a logical flaw in your code: you look for the first time ce_charttime > ne_charttime and then take the previous row. If there's no such time, you'll never have the chance to take the previous row, hence the NaNs in your result table starting from row 8.
PPS: This includes ce_charttime in the final dataframe. You can replace it by a column of how old the information is and/or remove it:
final_df['info_age'] = final_df.ne_charttime - final_df.ce_charttime
final_df = final_df.drop(columns='ce_charttime')
UPDATE for EDIT-2: As I wrote at the very beginning, repeated in the comments and as the docs clearly states: both ce_charttime and ne_charttime must be sorted (hadm_id need not be sorted). If this condition is not met, you'll have to (temporarily) sort your dataframes as required. See the following example:
import pandas as pd, string
df_str = pd.DataFrame( {'hadm_id': pd.np.tile([111111, 222222],10), 'ce_charttime': pd.date_range('2019-10-01 00:30', periods=20, freq='30T'), 'hr': pd.np.random.randint(80,120,20)})
df_notes = pd.DataFrame( {'hadm_id': pd.np.tile([111111, 222222],3), 'ne_charttime': pd.date_range('2019-10-01 00:45', periods=6, freq='40T'), 'note': [''.join(pd.np.random.choice(list(string.ascii_letters), 10)) for _ in range(6)]}).sort_values('hadm_id')
final_df = pd.merge_asof(df_notes.sort_values('ne_charttime'), df_str, left_on='ne_charttime', right_on='ce_charttime', by='hadm_id').sort_values(['hadm_id', 'ne_charttime'])
print(df_str); print(df_notes); print(final_df)
Output:
hadm_id ce_charttime hr
0 111111 2019-10-01 00:30:00 118
1 222222 2019-10-01 01:00:00 93
2 111111 2019-10-01 01:30:00 92
3 222222 2019-10-01 02:00:00 86
4 111111 2019-10-01 02:30:00 88
5 222222 2019-10-01 03:00:00 86
6 111111 2019-10-01 03:30:00 106
7 222222 2019-10-01 04:00:00 91
8 111111 2019-10-01 04:30:00 109
9 222222 2019-10-01 05:00:00 95
10 111111 2019-10-01 05:30:00 113
11 222222 2019-10-01 06:00:00 92
12 111111 2019-10-01 06:30:00 104
13 222222 2019-10-01 07:00:00 83
14 111111 2019-10-01 07:30:00 114
15 222222 2019-10-01 08:00:00 98
16 111111 2019-10-01 08:30:00 110
17 222222 2019-10-01 09:00:00 89
18 111111 2019-10-01 09:30:00 98
19 222222 2019-10-01 10:00:00 109
hadm_id ne_charttime note
0 111111 2019-10-01 00:45:00 jOcRWVdPDF
2 111111 2019-10-01 02:05:00 mvScJNrwra
4 111111 2019-10-01 03:25:00 FBAFbJYflE
1 222222 2019-10-01 01:25:00 ilNuInOsYZ
3 222222 2019-10-01 02:45:00 ysyolaNmkV
5 222222 2019-10-01 04:05:00 wvowGGETaP
hadm_id ne_charttime note ce_charttime hr
0 111111 2019-10-01 00:45:00 jOcRWVdPDF 2019-10-01 00:30:00 118
2 111111 2019-10-01 02:05:00 mvScJNrwra 2019-10-01 01:30:00 92
4 111111 2019-10-01 03:25:00 FBAFbJYflE 2019-10-01 02:30:00 88
1 222222 2019-10-01 01:25:00 ilNuInOsYZ 2019-10-01 01:00:00 93
3 222222 2019-10-01 02:45:00 ysyolaNmkV 2019-10-01 02:00:00 86
5 222222 2019-10-01 04:05:00 wvowGGETaP 2019-10-01 04:00:00 91
You can do full merge and then filter with query:
df_notes.merge(df_str, on=hadm_id).query('ce_charttime <= ne_charttime')
Source:
import pandas as pd
import numpy as np
cols = ['Date', 'Time', 'Load', 'Battery', 'Panel',
'Wind', 'Temp', 'Humidity', 'Volt']
data = pd.read_csv('test.csv',delimiter=';',header=0,names=cols,
decimal=',',parse_dates[[0,1]],
infer_datetime_format=True)
data.set_index('Date_Time',inplace=True)
I have this data frame:
In [126]: data.head()
Out[126]:
Load Battery Panel Wind Temp Humidity Volt
Date_Time
2018-07-31 13:07:15 13.3 326.3 353.1 0.98 33.93 21.92 3.89
2018-07-31 13:08:15 14.0 314.4 342.5 0.59 33.88 21.84 3.88
2018-07-31 13:09:16 13.4 309.6 335.5 0.39 33.84 22.14 3.88
2018-07-31 13:10:16 13.8 285.1 313.8 2.55 33.71 23.18 3.88
2018-07-31 13:11:16 13.6 292.9 314.7 2.03 33.62 23.25 3.88
......
with other 93000 rows. from 2018-07-31 to 2018-04-10. I'd like to resample by taking the sum of values for each 10minute frame. So I tried:
In [127]: data.resample('10min',closed='left',label='left').sum()
Out[127]:
Load Battery Panel Wind Temp Humidity Volt
Date_Time
2018-01-08 00:00:00 136.9 -140.6 -2.9 19.06 291.27 245.63 39.45
2018-01-08 00:10:00 137.3 -140.7 -3.1 15.14 290.62 244.88 39.42
2018-01-08 00:20:00 137.4 -140.4 -2.3 18.03 288.61 246.44 39.44
2018-01-08 00:30:00 137.5 -140.4 -2.2 12.61 286.97 246.83 39.43
That is close to what I expect, but the 'resample' remove all the data from the first day (I suspect maybe because the series do not start at midnight), what is the proper way to do the resampling? There are two issues:
The first day is missing in the result, i.e. all data removed and the resampled dataframe starts in the first of august and not on 07/31.
It is ok to consider intervals that starts at midnight and are so, perfectly multiple of 10min (so, ok for 00:00, 10:00, 20:00) but then I expect that the first grouping is:
2018-07-31 13:07:15 13.3 326.3 353.1 0.98 33.93 21.92 3.89
2018-07-31 13:08:15 14.0 314.4 342.5 0.59 33.88 21.84 3.88
2018-07-31 13:09:16 13.4 309.6 335.5 0.39 33.84 22.14 3.88
and then from 13:10:16, of course in the first day of the dataset and not on the second.
Ok. I solved it using:
x = data['2018-07-31'].resample('10min').sum()
y = data.resample('10min',closed='left',label='left').sum()
r = pd.concat([x,y])
but I think that this must be a form of bug in resample.
For output that starts at exactly 2018-07-31 13:07:15, you need to add in the argument base: "the origin of the aggregated intervals": documentation.
Example code:
start = pd.to_datetime('2018-07-31 13:07:15', format='%Y-%m-%d %H:%M:%S')
minutes = pd.date_range(start, start + timedelta(10), freq='min')
df = pd.DataFrame({'Date_Time': minutes, 'Load': np.random.randint(13, size=len(minutes))})
df.set_index('Date_Time', inplace=True)
df.resample('10min', closed='left', label='left', base=7.25).sum()
Result:
Date_Time Load
2018-07-31 13:07:15 11
2018-07-31 13:17:15 1
2018-07-31 13:27:15 6