Accessing a table¶
Accessing the table properties and data is straightforward and is generally consistent with
the basic interface for numpy structured arrays.
Warning
Astropy 2.0 introduces an API change that affects comparison of bytestring column elements in Python 3. See Bytestring columns in Python 3 for details.
Quick overview¶
For the impatient, the code below shows the basics of accessing table data. Where relevant there is a comment about what sort of object is returned. Except where noted, table access returns objects that can be modified in order to update the original table data or properties. See also the section on Copy versus Reference to learn more about this topic.
Make table
from astropy.table import Table
import numpy as np
arr = np.arange(15).reshape(5, 3)
t = Table(arr, names=('a', 'b', 'c'), meta={'keywords': {'key1': 'val1'}})
Table properties
t.columns # Dict of table columns (access by column name, index, or slice)
t.colnames # List of column names
t.meta # Dict of meta-data
len(t) # Number of table rows
Access table data
t['a'] # Column 'a'
t['a'][1] # Row 1 of column 'a'
t[1] # Row obj for with row 1 values
t[1]['a'] # Column 'a' of row 1
t[2:5] # Table object with rows 2:5
t[[1, 3, 4]] # Table object with rows 1, 3, 4 (copy)
t[np.array([1, 3, 4])] # Table object with rows 1, 3, 4 (copy)
t[[]] # Same table definition but with no rows of data
t['a', 'c'] # Table with cols 'a', 'c' (copy)
dat = np.array(t) # Copy table data to numpy structured array object
t['a'].quantity # an astropy.units.Quantity for Column 'a'
t['a'].to('km') # an astropy.units.Quantity for Column 'a' in units of kilometers
t.columns[1] # Column 1 (which is the 'b' column)
t.columns[0:2] # New table with columns 0 and 1
Note
Although they appear nearly equivalent, there is a factor of two performance
difference between t[1]['a'] (slower, because an intermediate Row
object gets created) versus t['a'][1] (faster). Always use the latter
when possible.
Print table or column
print(t) # Print formatted version of table to the screen
t.pprint() # Same as above
t.pprint(show_unit=True) # Show column unit
t.pprint(show_name=False) # Do not show column names
t.pprint(max_lines=-1, max_width=-1) # Print full table no matter how long / wide it is
t.more() # Interactively scroll through table like Unix "more"
print(t['a']) # Formatted column values
t['a'].pprint() # Same as above, with same options as Table.pprint()
t['a'].more() # Interactively scroll through column
lines = t.pformat() # Formatted table as a list of lines (same options as pprint)
lines = t['a'].pformat() # Formatted column values as a list
Details¶
For all the following examples it is assumed that the table has been created as below:
>>> from astropy.table import Table, Column
>>> import numpy as np
>>> import astropy.units as u
>>> arr = np.arange(15, dtype=np.int32).reshape(5, 3)
>>> t = Table(arr, names=('a', 'b', 'c'), meta={'keywords': {'key1': 'val1'}})
>>> t['a'].format = "%6.3f" # print as a float with 3 digits after decimal point
>>> t['a'].unit = 'm sec^-1'
>>> t['a'].description = 'unladen swallow velocity'
>>> print(t)
a b c
m sec^-1
-------- --- ---
0.000 1 2
3.000 4 5
6.000 7 8
9.000 10 11
12.000 13 14
Summary information¶
You can get summary information about the table as follows:
>>> t.info
<Table length=5>
name dtype unit format description
---- ----- -------- ------ ------------------------
a int32 m sec^-1 %6.3f unladen swallow velocity
b int32
c int32
If called as a function then one can supply an option that specifies
the type of information to return. The built-in option choices are
attributes (column attributes, which is the default) or stats
(basic column statistics). The option argument can also be a list
of available options:
>>> t.info('stats')
<Table length=5>
name mean std min max
---- ---- ------------- --- ---
a 6.0 4.24264068712 0 12
b 7.0 4.24264068712 1 13
c 8.0 4.24264068712 2 14
>>> t.info(['attributes', 'stats'])
<Table length=5>
name dtype unit format description mean std min max
---- ----- -------- ------ ------------------------ ---- ------------- --- ---
a int32 m sec^-1 %6.3f unladen swallow velocity 6.0 4.24264068712 0 12
b int32 7.0 4.24264068712 1 13
c int32 8.0 4.24264068712 2 14
Columns also have an info property that has the behavior and arguments,
but provides information about a single column:
>>> t['a'].info
name = a
dtype = int32
unit = m sec^-1
format = %6.3f
description = unladen swallow velocity
class = Column
n_bad = 0
length = 5
>>> t['a'].info('stats')
name = a
mean = 6.0
std = 4.24264068712
min = 0
max = 12
n_bad = 0
length = 5
Accessing properties¶
The code below shows accessing the table columns as a TableColumns object,
getting the column names, table meta-data, and number of table rows. The table
meta-data is simply an ordered dictionary (OrderedDict) by default.
>>> t.columns
<TableColumns names=('a','b','c')>
>>> t.colnames
['a', 'b', 'c']
>>> t.meta # Dict of meta-data
{'keywords': {'key1': 'val1'}}
>>> len(t)
5
Accessing data¶
As expected you can access a table column by name and get an element from that column with a numerical index:
>>> t['a'] # Column 'a'
<Column name='a' dtype='int32' unit='m sec^-1' format='%6.3f' description='unladen swallow velocity' length=5>
0.000
3.000
6.000
9.000
12.000
>>> t['a'][1] # Row 1 of column 'a'
3
When a table column is printed, it is formatted according to the format
attribute (see Format specifier). Note the difference between the
column representation above and how it appears via print() or str():
>>> print(t['a'])
a
m sec^-1
--------
0.000
3.000
6.000
9.000
12.000
Likewise a table row and a column from that row can be selected:
>>> t[1] # Row object corresponding to row 1
<Row index=1>
a b c
m sec^-1
int32 int32 int32
-------- ----- -----
3.000 4 5
>>> t[1]['a'] # Column 'a' of row 1
3
A Row object has the same columns and meta-data as its parent table:
>>> t[1].columns
<TableColumns names=('a','b','c')>
>>> t[1].colnames
['a', 'b', 'c']
Slicing a table returns a new table object which references to the original data within the slice region (See Copy versus Reference). The table meta-data and column definitions are copied.
>>> t[2:5] # Table object with rows 2:5 (reference)
<Table length=3>
a b c
m sec^-1
int32 int32 int32
-------- ----- -----
6.000 7 8
9.000 10 11
12.000 13 14
It is possible to select table rows with an array of indexes or by specifying multiple column names. This returns a copy of the original table for the selected rows or columns.
>>> print(t[[1, 3, 4]]) # Table object with rows 1, 3, 4 (copy)
a b c
m sec^-1
-------- --- ---
3.000 4 5
9.000 10 11
12.000 13 14
>>> print(t[np.array([1, 3, 4])]) # Table object with rows 1, 3, 4 (copy)
a b c
m sec^-1
-------- --- ---
3.000 4 5
9.000 10 11
12.000 13 14
>>> print(t['a', 'c']) # or t[['a', 'c']] or t[('a', 'c')]
... # Table with cols 'a', 'c' (copy)
a c
m sec^-1
-------- ---
0.000 2
3.000 5
6.000 8
9.000 11
12.000 14
We can select rows from a table using conditionals to create boolean masks. A
table indexed with a boolean array will only return rows where the mask array
element is True. Different conditionals can be combined using the bitwise
operators.
>>> mask = (t['a'] > 4) & (t['b'] > 8) # Table rows where column a > 4
>>> print(t[mask]) # and b > 8
...
a b c
m sec^-1
-------- --- ---
9.000 10 11
12.000 13 14
Finally, you can access the underlying table data as a native numpy
structured array by creating a copy or reference with np.array:
>>> data = np.array(t) # copy of data in t as a structured array
>>> data = np.array(t, copy=False) # reference to data in t
Formatted printing¶
The values in a table or column can be printed or retrieved as a formatted table using one of several methods:
print()function.- Table
more()or Columnmore()methods to interactively scroll through table values. - Table
pprint()or Columnpprint()methods to print a formatted version of the table to the screen. - Table
pformat()or Columnpformat()methods to return the formatted table or column as a list of fixed-width strings. This could be used as a quick way to save a table.
These methods use Format specifier if available and strive to make the output readable. By default, table and column printing will not print the table larger than the available interactive screen size. If the screen size cannot be determined (in a non-interactive environment or on Windows) then a default size of 25 rows by 80 columns is used. If a table is too large then rows and/or columns are cut from the middle so it fits. For example:
>>> arr = np.arange(3000).reshape(100, 30) # 100 rows x 30 columns array
>>> t = Table(arr)
>>> print(t)
col0 col1 col2 col3 col4 col5 col6 ... col23 col24 col25 col26 col27 col28 col29
---- ---- ---- ---- ---- ---- ---- ... ----- ----- ----- ----- ----- ----- -----
0 1 2 3 4 5 6 ... 23 24 25 26 27 28 29
30 31 32 33 34 35 36 ... 53 54 55 56 57 58 59
60 61 62 63 64 65 66 ... 83 84 85 86 87 88 89
90 91 92 93 94 95 96 ... 113 114 115 116 117 118 119
120 121 122 123 124 125 126 ... 143 144 145 146 147 148 149
150 151 152 153 154 155 156 ... 173 174 175 176 177 178 179
180 181 182 183 184 185 186 ... 203 204 205 206 207 208 209
210 211 212 213 214 215 216 ... 233 234 235 236 237 238 239
240 241 242 243 244 245 246 ... 263 264 265 266 267 268 269
270 271 272 273 274 275 276 ... 293 294 295 296 297 298 299
... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
2670 2671 2672 2673 2674 2675 2676 ... 2693 2694 2695 2696 2697 2698 2699
2700 2701 2702 2703 2704 2705 2706 ... 2723 2724 2725 2726 2727 2728 2729
2730 2731 2732 2733 2734 2735 2736 ... 2753 2754 2755 2756 2757 2758 2759
2760 2761 2762 2763 2764 2765 2766 ... 2783 2784 2785 2786 2787 2788 2789
2790 2791 2792 2793 2794 2795 2796 ... 2813 2814 2815 2816 2817 2818 2819
2820 2821 2822 2823 2824 2825 2826 ... 2843 2844 2845 2846 2847 2848 2849
2850 2851 2852 2853 2854 2855 2856 ... 2873 2874 2875 2876 2877 2878 2879
2880 2881 2882 2883 2884 2885 2886 ... 2903 2904 2905 2906 2907 2908 2909
2910 2911 2912 2913 2914 2915 2916 ... 2933 2934 2935 2936 2937 2938 2939
2940 2941 2942 2943 2944 2945 2946 ... 2963 2964 2965 2966 2967 2968 2969
2970 2971 2972 2973 2974 2975 2976 ... 2993 2994 2995 2996 2997 2998 2999
Length = 100 rows
more() method¶
In order to browse all rows of a table or column use the Table
more() or Column more()
methods. These let you interactively scroll through the rows much like the
linux more command. Once part of the table or column is displayed the
supported navigation keys are:
pprint() method¶
In order to fully control the print output use the Table
pprint() or Column
pprint() methods. These have keyword
arguments max_lines, max_width, show_name, show_unit with
meaning as shown below:
>>> arr = np.arange(3000, dtype=float).reshape(100, 30)
>>> t = Table(arr)
>>> t['col0'].format = '%e'
>>> t['col1'].format = '%.6f'
>>> t['col0'].unit = 'km**2'
>>> t['col29'].unit = 'kg sec m**-2'
>>> t.pprint(max_lines=8, max_width=40)
col0 ... col29
km2 ... kg sec m**-2
------------ ... ------------
0.000000e+00 ... 29.0
... ... ...
2.940000e+03 ... 2969.0
2.970000e+03 ... 2999.0
Length = 100 rows
>>> t.pprint(max_lines=8, max_width=40, show_unit=True)
col0 ... col29
km2 ... kg sec m**-2
------------ ... ------------
0.000000e+00 ... 29.0
... ... ...
2.940000e+03 ... 2969.0
2.970000e+03 ... 2999.0
Length = 100 rows
>>> t.pprint(max_lines=8, max_width=40, show_name=False)
km2 ... kg sec m**-2
------------ ... ------------
0.000000e+00 ... 29.0
3.000000e+01 ... 59.0
... ... ...
2.940000e+03 ... 2969.0
2.970000e+03 ... 2999.0
Length = 100 rows
In order to force printing all values regardless of the output length or width
set max_lines or max_width to -1, respectively. For the wide
table in this example you see 6 lines of wrapped output like the following:
>>> t.pprint(max_lines=8, max_width=-1)
col0 col1 col2 col3 col4 col5 col6 col7 col8 col9 col10 col11 col12 col13 col14 col15 col16 col17 col18 col19 col20 col21 col22 col23 col24 col25 col26 col27 col28 col29
km2 kg sec m**-2
------------ ----------- ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------------
0.000000e+00 1.000000 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 10.0 11.0 12.0 13.0 14.0 15.0 16.0 17.0 18.0 19.0 20.0 21.0 22.0 23.0 24.0 25.0 26.0 27.0 28.0 29.0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
2.940000e+03 2941.000000 2942.0 2943.0 2944.0 2945.0 2946.0 2947.0 2948.0 2949.0 2950.0 2951.0 2952.0 2953.0 2954.0 2955.0 2956.0 2957.0 2958.0 2959.0 2960.0 2961.0 2962.0 2963.0 2964.0 2965.0 2966.0 2967.0 2968.0 2969.0
2.970000e+03 2971.000000 2972.0 2973.0 2974.0 2975.0 2976.0 2977.0 2978.0 2979.0 2980.0 2981.0 2982.0 2983.0 2984.0 2985.0 2986.0 2987.0 2988.0 2989.0 2990.0 2991.0 2992.0 2993.0 2994.0 2995.0 2996.0 2997.0 2998.0 2999.0
Length = 100 rows
For columns the syntax and behavior of
pprint() is the same except that there is no
max_width keyword argument:
>>> t['col3'].pprint(max_lines=8)
col3
------
3.0
33.0
...
2943.0
2973.0
Length = 100 rows
Column alignment¶
Individual columns have the ability to be aligned in a number of different ways, for an enhanced viewing experience:
>>> t1 = Table()
>>> t1['long column name 1'] = [1, 2, 3]
>>> t1['long column name 2'] = [4, 5, 6]
>>> t1['long column name 3'] = [7, 8, 9]
>>> t1['long column name 4'] = [700000, 800000, 900000]
>>> t1['long column name 2'].format = '<'
>>> t1['long column name 3'].format = '0='
>>> t1['long column name 4'].format = '^'
>>> t1.pprint()
long column name 1 long column name 2 long column name 3 long column name 4
------------------ ------------------ ------------------ ------------------
1 4 000000000000000007 700000
2 5 000000000000000008 800000
3 6 000000000000000009 900000
Conveniently, alignment can be handled another way, by passing a list to the
keyword argument align:
>>> t1 = Table()
>>> t1['column1'] = [1, 2, 3]
>>> t1['column2'] = [2, 4, 6]
>>> t1.pprint(align=['<', '0='])
column1 column2
------- -------
1 0000002
2 0000004
3 0000006
It is also possible to set the alignment of all columns with a single string value:
>>> t1.pprint(align='^')
column1 column2
------- -------
1 2
2 4
3 6
The fill character for justification can be set as a prefix to the
alignment character (see Format Specification Mini-Language
for additional explanation). This can be done both in the align argument
and in the column format attribute. Note the interesting interaction below:
>>> t1 = Table([[1.0, 2.0], [1, 2]], names=['column1', 'column2'])
>>> t1['column1'].format = '#^.2f'
>>> t1.pprint()
column1 column2
------- -------
##1.00# 1
##2.00# 2
Now if we set a global align, it seems like our original column format got lost:
>>> t1.pprint(align='!<')
column1 column2
------- -------
1.00!!! 1!!!!!!
2.00!!! 2!!!!!!
The way to avoid this is to explicitly specify the alignment strings
for every column and use None where the column format should be
used:
>>> t1.pprint(align=[None, '!<'])
column1 column2
------- -------
##1.00# 1!!!!!!
##2.00# 2!!!!!!
pformat() method¶
In order to get the formatted output for manipulation or writing to a file use
the Table pformat() or Column
pformat() methods. These behave just as for
pprint() but return a list corresponding to each formatted line in the
pprint() output.
>>> lines = t['col3'].pformat(max_lines=8)
Multidimensional columns¶
If a column has more than one dimension then each element of the column is
itself an array. In the example below there are 3 rows, each of which is a
2 x 2 array. The formatted output for such a column shows only the first
and last value of each row element and indicates the array dimensions in the
column name header:
>>> from astropy.table import Table, Column
>>> import numpy as np
>>> t = Table()
>>> arr = [ np.array([[ 1, 2],
... [10, 20]]),
... np.array([[ 3, 4],
... [30, 40]]),
... np.array([[ 5, 6],
... [50, 60]]) ]
>>> t['a'] = arr
>>> t['a'].shape
(3, 2, 2)
>>> t.pprint()
a [2,2]
-------
1 .. 20
3 .. 40
5 .. 60
In order to see all the data values for a multidimensional column use the
column representation. This uses the standard numpy mechanism for printing
any array:
>>> t['a'].data
array([[[ 1, 2],
[10, 20]],
[[ 3, 4],
[30, 40]],
[[ 5, 6],
[50, 60]]])
Columns with Units¶
A Column object with units within a standard
Table (as opposed to a QTable) has certain
quantity-related conveniences available. To begin with, it can be converted
explicitly to a Quantity object via the
quantity property and the
to() method:
>>> data = [[1., 2., 3.], [40000., 50000., 60000.]]
>>> t = Table(data, names=('a', 'b'))
>>> t['a'].unit = u.m
>>> t['b'].unit = 'km/s'
>>> t['a'].quantity
<Quantity [1., 2., 3.] m>
>>> t['b'].to(u.kpc/u.Myr)
<Quantity [40.9084866 , 51.13560825, 61.3627299 ] kpc / Myr>
Note that the quantity property is actually
a view of the data in the column, not a copy. Hence, you can set the
values of a column in a way that respects units by making in-place
changes to the quantity property:
>>> t['b']
<Column name='b' dtype='float64' unit='km / s' length=3>
40000.0
50000.0
60000.0
>>> t['b'].quantity[0] = 45000000*u.m/u.s
>>> t['b']
<Column name='b' dtype='float64' unit='km / s' length=3>
45000.0
50000.0
60000.0
Even without explicit conversion, columns with units can be treated like
like an Astropy Quantity in some arithmetic
expressions (see the warning below for caveats to this):
>>> t['a'] + .005*u.km
<Quantity [6., 7., 8.] m>
>>> from astropy.constants import c
>>> (t['b'] / c).decompose()
<Quantity [0.15010384, 0.16678205, 0.20013846]>
Warning
Table columns do not always behave the same as
Quantity. Table columns act more like regular numpy
arrays unless either explicitly converted to a
Quantity or combined with an
Quantity using an arithmetic operator.For example,
the following does not work the way you would expect:
>>> import numpy as np
>>> from astropy.table import Table
>>> data = [[30, 90]]
>>> t = Table(data, names=('angle',))
>>> t['angle'].unit = 'deg'
>>> np.sin(t['angle'])
<Column name='angle' dtype='float64' unit='deg' length=2>
-0.988031624093
0.893996663601
This is wrong both in that it says the unit is degrees, and sin treated
the values and radians rather than degrees. If at all in doubt that you’ll
get the right result, the safest choice is to either use
QTable or to explicitly convert to
Quantity:
>>> np.sin(t['angle'].quantity)
<Quantity [0.5, 1. ]>
Bytestring columns in Python 3¶
Prior to astropy 2.0, using bytestring columns (numpy 'S' dtype) in Python
3 was inconvenient because it was not possible to compare with the natural
Python string (str) type. See The bytes/str dichotomy in Python 3
for a very brief overview of the difference.
The standard method of representing Python 3 strings in numpy is via the
unicode 'U' dtype. The problem is that this requires 4 bytes per
character, and if you have a very large number of strings in memory this could
fill memory and impact performance. A very common use case is that these
strings are actually ASCII and can be represented with 1 byte per character.
Starting with astropy 2.0 it is possible to work directly and conveniently with
bytestring data in astropy Table and Column
Note that the bytestring issue is a particular problem when dealing with HDF5
files, where character data are read as bytestrings ('S' dtype) when using
the Unified file read/write interface. Since HDF5 files are frequently used to store very large
datasets, the memory bloat associated with conversion to 'U' dtype is
unacceptable.
Python 3 examples¶
The examples below highlight the change in behavior introduced by astropy 2.0
for Python 3. In particular please note the API change when comparing with a
single element of a bytestring column. Previously one was required to compare
with a bytes object while now one must compare with a str object. When
comparing with the entire column one can use either a bytes or str.
Before astropy 2.0
>>> from astropy.table import Table
>>> t = Table([['abc', 'def']], names=['a'], dtype=['S'])
>>> t['a'] == 'abc' # WRONG answer!
False
>>> t['a'] == b'abc' # Must explicitly compare to bytestring
array([ True, False], dtype=bool)
>>> t = Table([['bä', 'def']], dtype=['S'])
Traceback (most recent call last):
...
UnicodeEncodeError: 'ascii' codec can't encode character '\xe4' in position 1:
ordinal not in range(128)
Astropy 2.0 or later:
>>> t = Table([['abc', 'def']], names=['a'], dtype=['S'])
>>> t['a'] == 'abc' # Gives expected answer
array([ True, False], dtype=bool)
>>> t['a'] == b'abc' # Still gives expected answer
array([ True, False], dtype=bool)
>>> t['a'][0] == 'abc' # Expected answer
True
>>> t['a'][0] == b'abc' # API change, this NO LONGER WORKS
False
>>> t['a'][0] = 'bä'
>>> t
<Table length=2>
a
bytes3
------
bä
def
>>> t['a'] == 'bä'
array([ True, False], dtype=bool)
>>> # Round trip unicode strings through HDF5
>>> t = Table([['bä', 'def']], dtype=['S'])
>>> t.write('test.hdf5', format='hdf5', path='data', overwrite=True)
>>> t2 = Table.read('test.hdf5', format='hdf5', path='data')
>>> t2
<Table length=2>
col0
bytes3
------
bä
def