Create Structured Numpy Array with Different Types

Question

I have the following unstructured data (read from a csv).

data = [[b'id' b'datetime' b'anomaly_length' b'affected_sensors' b'reason']
 [b'1' b'2019-12-20 08:09' b'26' b'all' b'Open Windows']
 [b'1' b'2019-12-20 08:10' b'26' b'all' b'Open Windows']
 [b'1' b'2019-12-20 08:11' b'26' b'all' b'Open Windows']
 [b'1' b'2019-12-20 08:12' b'26' b'all' b'Open Windows']
 [b'1' b'2019-12-20 08:13' b'26' b'all' b'Open Windows']
 [b'1' b'2019-12-20 08:14' b'26' b'all' b'Open Windows']
 [b'1' b'2019-12-20 08:15' b'26' b'all' b'Open Windows']
 [b'1' b'2019-12-20 08:16' b'26' b'all' b'Open Windows']
 [b'1' b'2019-12-20 08:17' b'26' b'all' b'Open Windows']]
 ...

I currently create structured arrays by using the following code:

labels_id = np.array(data[1:,0], dtype=int)
labels = [dt.datetime.strptime(date.decode("utf-8"), '%Y-%m-%d %H:%M') for date in np.array(data[1:,1])]
labels_length = np.array(data[1:,2], dtype=int)

This code is necessary because I need data with the correct datatype. In the function, I pass all the arrays and access them by index. I don't like this solution but because the function is called multiple times I don't want to cast the data inside the function each time.

Origin function code:

def special_find(labels_id, labels, labels_length):
    for i, id in enumerate(labels_id):
       print(id)
       print(labels[i])
       print(labels_length[i])
...

Expected: I want to have a structured array which only contains the needed columns:

structured_data = [[1 datetime.datetime(2019, 12, 20, 8, 9) b'2019-12-20 08:09' 26],
 [1 datetime.datetime(2019, 12, 20, 8, 10) 26],
 [1 datetime.datetime(2019, 12, 20, 8, 11) 26],
 [1 datetime.datetime(2019, 12, 20, 8, 12) 26],
 [1 datetime.datetime(2019, 12, 20, 8, 13) 26],
 [1 datetime.datetime(2019, 12, 20, 8, 14) 26],
...

I know I could concat all the created arrays but I don't think this is a good solution. Instead, I am searching for something like this:

structured_data = np.array(data[1:, 0:3], dtype=...)

UPDATE: here are some values for a csv file

id,datetime,anomaly_length,affected_sensors,reason
1,2019-12-20 08:09,26,all,Open Windows
1,2019-12-20 08:10,26,all,Open Windows
1,2019-12-20 08:11,26,all,Open Windows
1,2019-12-20 08:12,26,all,Open Windows
1,2019-12-20 08:13,26,all,Open Windows
1,2019-12-20 08:14,26,all,Open Windows
1,2019-12-20 08:15,26,all,Open Windows
1,2019-12-20 08:16,26,all,Open Windows
1,2019-12-20 08:17,26,all,Open Windows

Use Pandas. NumPy loses lots of its usefulness when your data isn't all of the same type. — Seb
– Seb, Commented Jan 9, 2020 at 14:03
It might be easier to get the structured array when reading the csv. You can specify dtype=None or your own dtype — hpaulj
– hpaulj, Commented Jan 9, 2020 at 17:03
The pandas read_csv is powerful and fast. You could use ``to_records` to get a structured array from the dataframe. Regardless handing that date/time column can be tricky, since possible types include string, datetime objects and np.datetime64. — hpaulj
– hpaulj, Commented Jan 9, 2020 at 19:33
I'll second what @Seb suggested, use Pandas. Can you share at least part of your data? See: minimal reproducible example. — AMC
– AMC, Commented Jan 10, 2020 at 0:12

Seb · Accepted Answer · 2020-01-09 14:33:09Z

1

Since you've already converted the columns to NumPy arrays of the correct data type, it is easy to create a Pandas DataFrame from them, for example:

import pandas as pd

df = pd.DataFrame({
    'id': labels_id,
    'datetime': labels,
    'anomaly_length': labels_length
})

>>> df
   id            datetime  anomaly_length
0   1 2019-12-20 08:09:00              26
1   1 2019-12-20 08:10:00              26
2   1 2019-12-20 08:11:00              26
3   1 2019-12-20 08:12:00              26
4   1 2019-12-20 08:13:00              26
5   1 2019-12-20 08:14:00              26
6   1 2019-12-20 08:15:00              26
7   1 2019-12-20 08:16:00              26
8   1 2019-12-20 08:17:00              26

The Pandas docs have a good introduction on how to work with these objects.

answered Jan 9, 2020 at 14:33

Seb

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2 Comments

wake-0 Over a year ago

Is it possible to use pandas directly for reading the csv and filling the dataframe?

stepuncius Over a year ago

@KevinWallis yes, pandas.pydata.org/pandas-docs/stable/reference/api/…

hpaulj · Accepted Answer · 2020-01-09 19:42:54Z

I tried to recreate your csv file with:

In [23]: cat stack59665655.txt                                                  
id, datetime, anomaly_length, affected_sensors, reason
1, 2019-12-20 08:09, 26, all, Open Windows
1, 2019-12-20 08:10, 26, all, Open Windows
1, 2019-12-20 08:11, 26, all, Open Windows

With pandas I can read it with:

In [24]: data = pd.read_csv('stack59665655.txt')                                
In [25]: data                                                                   
Out[25]: 
   id           datetime   anomaly_length  affected_sensors         reason
0   1   2019-12-20 08:09               26               all   Open Windows
1   1   2019-12-20 08:10               26               all   Open Windows
2   1   2019-12-20 08:11               26               all   Open Windows
In [26]: data.dtypes                                                            
Out[26]: 
id                    int64
 datetime            object
 anomaly_length       int64
 affected_sensors    object
 reason              object
dtype: object

The object columns contain strings. I suspect pandas has a way of converting that datetime string column to datetime objects or np.datetime64.

The simple conversion to array, produces an object dtype array:

In [27]: data.to_numpy()                                                        
Out[27]: 
array([[1, ' 2019-12-20 08:09', 26, ' all', ' Open Windows'],
       [1, ' 2019-12-20 08:10', 26, ' all', ' Open Windows'],
       [1, ' 2019-12-20 08:11', 26, ' all', ' Open Windows']],
      dtype=object)

to_records produces a record array, a variant on a structured array. Note the compound dtype:

In [28]: data.to_records()                                                      
Out[28]: 
rec.array([(0, 1, ' 2019-12-20 08:09', 26, ' all', ' Open Windows'),
           (1, 1, ' 2019-12-20 08:10', 26, ' all', ' Open Windows'),
           (2, 1, ' 2019-12-20 08:11', 26, ' all', ' Open Windows')],
          dtype=[('index', '<i8'), ('id', '<i8'), (' datetime', 'O'), (' anomaly_length', '<i8'), (' affected_sensors', 'O'), (' reason', 'O')])

Instead, using genfromtxt with it's auto-dtype mode:

In [29]: data1 =np.genfromtxt('stack59665655.txt',dtype=None, names=True,delimit
    ...: er=',',encoding=None, autostrip=True)                                  
In [30]: data1                                                                  
Out[30]: 
array([(1, '2019-12-20 08:09', 26, 'all', 'Open Windows'),
       (1, '2019-12-20 08:10', 26, 'all', 'Open Windows'),
       (1, '2019-12-20 08:11', 26, 'all', 'Open Windows')],
      dtype=[('id', '<i8'), ('datetime', '<U16'), ('anomaly_length', '<i8'), ('affected_sensors', '<U3'), ('reason', '<U12')])

I could convert the datetime field with:

In [31]: data1['datetime']                                                      
Out[31]: 
array(['2019-12-20 08:09', '2019-12-20 08:10', '2019-12-20 08:11'],
      dtype='<U16')
In [32]: data1['datetime'].astype('datetime64[m]')                              
Out[32]: 
array(['2019-12-20T08:09', '2019-12-20T08:10', '2019-12-20T08:11'],
      dtype='datetime64[m]')

Changing this in-place actually requires defining a new dtype.

Or I could construct a custom dtype, for example by modifying the one deduced for data1:

In [45]: dt = data1.dtype.descr                                                 
In [46]: dt[1]=('datetime', 'datetime64[m]')                                    
In [47]: dt= np.dtype(dt)                                                       
In [48]: dt                                                                     
Out[48]: dtype([('id', '<i8'), ('datetime', '<M8[m]'), ('anomaly_length', '<i8'), ('affected_sensors', '<U3'), ('reason', '<U12')])

In [49]: data2 =np.genfromtxt('stack59665655.txt',dtype=dt, names=True,delimiter
    ...: =',',encoding=None, autostrip=True)                                    
In [50]: data2                                                                  
Out[50]: 
array([(1, '2019-12-20T08:09', 26, 'all', 'Open Windows'),
       (1, '2019-12-20T08:10', 26, 'all', 'Open Windows'),
       (1, '2019-12-20T08:11', 26, 'all', 'Open Windows')],
      dtype=[('id', '<i8'), ('datetime', '<M8[m]'), ('anomaly_length', '<i8'), ('affected_sensors', '<U3'), ('reason', '<U12')])

To use datetime objects, I'd have to use a converter in `genfromtxt.

I suspect pandas has a way of converting that datetime string column to datetime objects or np.datetime64 .read_csv() has a parse_dates parameter, that might work?
thanks for the answer I actually combined read_csv with converters

wake-0 · Accepted Answer · 2020-01-10 09:03:09Z

0

I combined the read_csv from pandas together with `converters:

import pandas as pd
import datetime as dt

filename = './data.csv'

to_date = lambda value: (dt.datetime.strptime(value, '%Y-%m-%d %H:%M'))
values = pd.read_csv(filename, converters={'datetime': to_date})
print(values.dtypes)


>>> OUTPUT:
>>> id                           int64
>>> datetime            datetime64[ns]
>>> anomaly_length               int64
>>> affected_sensors            object
>>> reason                      object
>>> dtype: object

answered Jan 10, 2020 at 9:03

wake-0

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