Modifying a table¶

The data values within a Table object can be modified in much the same manner as for numpy structured arrays by accessing columns or rows of data and assigning values appropriately. A key enhancement provided by the Table class is the ability to easily modify the structure of the table: one can add or remove columns, and add new rows of data.

Quick overview¶

The code below shows the basics of modifying a table and its data.

Make a 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'}})

Modify data values

>>> t['a'][:] = [1, -2, 3, -4, 5]  # Set all column values
>>> t['a'] = 30                 # Set row 2 of column 'a'
>>> t = (8, 9, 10)              # Set all row values
>>> t['b'] = -9                 # Set column 'b' of row 1
>>> t[0:3]['c'] = 100              # Set column 'c' of rows 0, 1, 2

Note that table[row][column] assignments will not work with numpy “fancy” row indexing (in that case table[row] would be a copy instead of a view). “Fancy” numpy indices include a list, numpy.ndarray, or tuple of numpy.ndarray (e.g. the return from numpy.where):

>>> t[[1, 2]]['a'] = [3., 5.]             # doesn't change table t
>>> t[np.array([1, 2])]['a'] = [3., 5.]   # doesn't change table t
>>> t[np.where(t['a'] > 3)]['a'] = 3.     # doesn't change table t

Instead use table[column][row] order:

>>> t['a'][[1, 2]] = [3., 5.]
>>> t['a'][np.array([1, 2])] = [3., 5.]
>>> t['a'][np.where(t['a'] > 3)] = 3.

You can also modify data columns with unit set in a way that follows the conventions of Quantity by using the quantity property:

>>> from astropy import units as u
>>> tu = Table([[1, 2.5]], names=('a',))
>>> tu['a'].unit = u.m
>>> tu['a'].quantity[:] = [1, 2] * u.km
>>> tu['a']
<Column name='a' dtype='float64' unit='m' length=2>
1000.0
2000.0

Add a column or columns

A single column can be added to a table using syntax like adding a dict value. The value on the right hand side can be a list or array of the correct size, or a scalar value that will be broadcast:

>>> t['d1'] = np.arange(5)
>>> t['d2'] = [1, 2, 3, 4, 5]
>>> t['d3'] = 6  # all 5 rows set to 6

For more explicit control the add_column() and add_columns() methods can be used to add one or multiple columns to a table. In both cases the new columns must be specified as Column or MaskedColumn objects:

>>> from astropy.table import Column
>>> aa = Column(np.arange(5), name='aa')
>>> t.add_column(aa, index=0)  # Insert before the first table column
>>> bb = Column(np.arange(5))
>>> t.add_column(bb, name='bb')  # Append unnamed column to the table with 'bb' as name

# Make a new table with the same number of rows and add columns to original table
>>> t2 = Table(np.arange(25).reshape(5, 5), names=('e', 'f', 'g', 'h', 'i'))

Finally, columns can also be added from Quantity objects, which automatically sets the .unit attribute on the column:

>>> from astropy import units as u
>>> t['d'] = np.arange(1., 6.) * u.m
>>> t['d']
<Column name='d' dtype='float64' unit='m' length=5>
1.0
2.0
3.0
4.0
5.0

Remove columns

>>> t.remove_column('f')
>>> t.remove_columns(['aa', 'd1', 'd2', 'd3', 'e'])
>>> del t['g']
>>> del t['h', 'i']
>>> t.keep_columns(['a', 'b'])

Replace a column

One can entirely replace an existing column with a new column by setting the column to any object that could be used to initialize a table column (e.g. a list or numpy array). For example, one could change the data type of the a column from int to float using:

>>> t['a'] = t['a'].astype(float)

If the right hand side value is not column-like, then an in-place update using broadcasting will be done, e.g.:

>>> t['a'] = 1  # Internally does t['a'][:] = 1

Note

Prior to astropy version 1.3, assignment as shown above performed an in-place update of the existing column values and it was not possible to change the data type in this way. Prior to 1.3 it was necessary to use the replace_column() method in this case. See the section API change in replacing columns for additional information.

Rename columns

>>> t.rename_column('a', 'a_new')
>>> t['b'].name = 'b_new'

Add a row of data

Remove rows

>>> t.remove_row(0)
>>> t.remove_rows(slice(4, 5))
>>> t.remove_rows([1, 2])

Sort by one more more columns

>>> t.sort('b_new')
>>> t.sort(['a_new', 'b_new'])

Reverse table rows

>>> t.reverse()

Modify meta-data

>>> t.meta['key'] = 'value'

Select or reorder columns

A new table with a subset or reordered list of columns can be created as shown in the following example:

>>> t = Table(arr, names=('a', 'b', 'c'))
>>> t_acb = t['a', 'c', 'b']

Another way to do the same thing is to provide a list or tuple as the item as shown below:

>>> new_order = ['a', 'c', 'b']  # List or tuple
>>> t_acb = t[new_order]

Caveats¶

Modifying the table data and properties is fairly straightforward. One thing to keep in mind is that adding a row may require a new copy in memory of the table data. This depends on the detailed layout of Python objects in memory and cannot be reliably controlled. In some cases it may be possible to build a table row by row in less than O(N**2) time but you cannot count on it.

Another subtlety to keep in mind are cases where the return value of an operation results in a new table in memory versus a view of the existing table data. As an example, imagine trying to set two table elements using column selection with t['a', 'c'] in combination with row index selection:

>>> t = Table([[1, 2], [3, 4], [5, 6]], names=('a', 'b', 'c'))
>>> t['a', 'c'] = (100, 100)
>>> print(t)
a   b   c
--- --- ---
1   3   5
2   4   6

This might be surprising because the data values did not change and there was no error. In fact what happened is that t['a', 'c'] created a new temporary table in memory as a copy of the original and then updated row 1 of the copy. The original t table was unaffected and the new temporary table disappeared once the statement was complete. The takeaway is to pay attention to how certain operations are performed one step at a time.

API change in replacing columns¶

Astropy version 1.3 introduces an API change in the way that the following behaves:

>>> t = Table([[1, 2, 3]], names=['a'])
>>> t['a'] = [10.5, 20.5, 30.5]

Prior to 1.3 this always did an in-place replacement of the data values so that the t['a'] column object reference was maintained. However, since the original data type was integer in this case, the replaced values would silently be converted to integer by truncation.

Starting with astropy 1.3 the operation shown above does a complete replacement of the column object. In this case it makes a new column object with float values by internally calling t.replace_column('a', [10.5, 20.5, 30.5]). In general this behavior is more consistent with Python and Pandas behavior, but there is potential for somewhat subtle bugs in code that was written that expects the pre-1.3 in-place behavior. Therefore, a TableReplaceWarning will appear.

Examples

>>> t = Table([[1, 2, 3]], names=['a'])
>>> t['a'].description = 'My data column'

# Sliced column gets replaced
>>> t2 = t[:2]  # Make a slice

# In astropy 1.3 the following emits a warning about replacing a slice.
>>> t2['a'] = [10, 20]

>>> list(t['a'])  # Outputs [10, 20, 3] prior to astropy 1.3.
[1, 2, 3]

# Column reference count changes
>>> ta = t['a']  # Make a reference to the original column
>>> t['a'] = [10, 20, 30]
>>> t['a'] is ta  # Outputs True prior to astropy 1.3
False

# Column attributes change
>>> print(t['a'].description)  # Outputs 'My data column' prior to astropy 1.3
None

Replicating pre-1.3 behavior

If the pre-1.3 in-place behavior is required in code, it is straightforward to achieve this. Simply replace:

t[colname] = value

with:

t[colname][:] = value

As a temporary measure, or if the problematic code is in a package that cannot be modified, one can modify the table.replace_inplace configuration variable:

from astropy import table
table.conf.replace_inplace = True

This will entirely revert to the pre-1.3 behavior. This configuration option will be deprecated and then subsequently removed in future releases, so it is meant only as a stop-gap to provide time to appropriately update all code.

Finding the source of problems

In order to find potential problems related to the API change, the configuration option table.conf.replace_warnings controls a set of warnings that are emitted under certain circumstances when a table column is replaced. This option must be set to a list that includes zero or more of the following string values:

always :

Print a warning every time a column gets replaced via the setitem syntax (i.e. t['a'] = new_col).

slice :

Print a warning when a column that appears to be a slice of a parent column is replaced.

refcount :

Print a warning when the Python reference count for the column changes. This indicates that a stale object exists that might be used elsewhere in the code and give unexpected results.

attributes :

Print a warning if any of the standard column attributes changed.

The default value for the table.conf.replace_warnings option is ['slice'].