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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"

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<body>

<a class="brand" title="Documentation Home" href="../index.html">python4astronomers</a>

<ul>

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<ul>

</a>

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<a href="../index.html">Python4Astronomers 2.0 documentation</a>

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<li><a href="astropy.html" accesskey="U">Astropy I: core functions</a> »</li>

<li>Tabular data</li>

</ul>

</div>

<h1>Tabular data<a class="headerlink" href="#tabular-data" title="Permalink to this headline">¶</a></h1>

Astropy includes a class for representing arbitrary tabular data in

<tt class="docutils literal">astropy.table</tt>, called <tt class="docutils literal">Table</tt>. This class can be imported with:

<div class="highlight-python"><div class="highlight"><pre>from astropy.table import Table

</pre></div>

</div>

You may need to also import the <tt class="docutils literal">Column</tt> class, depending on how you are

definining your table (see below):

<div class="highlight-python"><div class="highlight"><pre>from astropy.table import Table, Column

</pre></div>

</div>

<h2>Documentation<a class="headerlink" href="#documentation" title="Permalink to this headline">¶</a></h2>

For more information about the features presented below, you can read the

<a class="reference external" href="http://docs.astropy.org/en/stable/table/index.html">astropy.table</a> docs.

</div>

<h2>Constructing and Manipulating tables<a class="headerlink" href="#constructing-and-manipulating-tables" title="Permalink to this headline">¶</a></h2>

There are a number of ways of constructing tables. One simple way is to start

from existing lists or arrays:

<div class="highlight-python"><div class="highlight"><pre>>>> from astropy.table import Table

>>> a = [1, 4, 5]

>>> b = [2.0, 5.0, 8.2]

>>> c = ['x', 'y', 'z']

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

</pre></div>

</div>

There are a few ways to examine the table. You can get detailed information

about the table values and column definitions as follows:

<div class="highlight-python"><div class="highlight"><pre>>>> t

array([(1, 2.0, 'x'), (4, 5.0, 'y'), (5, 8.2, 'z')],

dtype=[('a', '<i8'), ('b', '<f8'), ('c', '|S1')])

</pre></div>

</div>

If you print the table (either from the noteboook or in a text console

session) then a formatted version appears:

<div class="highlight-python"><div class="highlight"><pre>>>> print(t)

a b c

--- --- ---

1 2.0 x

4 5.0 y

5 8.2 z

</pre></div>

</div>

Now examine some high-level information about the table:

<div class="highlight-python"><div class="highlight"><pre>>>> t.colnames

['a', 'b', 'c']

>>> len(t)

3

</pre></div>

</div>

Access the data by column or row using the same syntax as for Numpy structured

arrays:

array([1, 4, 5])

>>> t['a'][1] # Row 1 of column 'a'

4

>>> t[1] # Row obj for with row 1 values

<Row 1 of table

values=(4, 5.0, 'y')

dtype=[('a', '<i8'), ('b', '<f8'), ('c', '|S1')]>

>>> t[1]['a'] # Column 'a' of row 1

4

</pre></div>

</div>

One can retrieve a subset of a table by rows (using a slice) or columns (using

column names), where the subset is returned as a new table:

<div class="highlight-python"><div class="highlight"><pre>>>> print(t[0:2]) # Table object with rows 0 and 1

a b c

--- --- ---

1 2.0 x

4 5.0 y

>>> t['a', 'c'] # Table with cols 'a', 'c'

a c

--- ---

1 x

4 y

5 z

</pre></div>

</div>

Modifying table values in place is flexible and works as one would expect:

<div class="highlight-python"><div class="highlight"><pre>>>> t['a'] = [-1, -2, -3] # Set all column values

>>> t['a'][2] = 30 # Set row 2 of column 'a'

>>> t[1] = (8, 9.0, "W") # Set all row values

>>> t[1]['b'] = -9 # Set column 'b' of row 1

>>> t[0:2]['b'] = 100.0 # Set column 'c' of rows 0 and 1

>>> print(t)

a b c

--- ----- ---

-1 100.0 x

8 100.0 W

30 8.2 z

</pre></div>

</div>

Add, remove, and rename columns with the following:

<div class="highlight-python"><div class="highlight"><pre>>>> t.add_column(Column(data=[1, 2, 3], name='d')))

>>> t.remove_column('c')

>>> t.rename_column('a', 'A')

>>> t.colnames

['A', 'b', 'd']

</pre></div>

</div>

Adding a new row of data to the table is as follows:

<div class="highlight-python"><div class="highlight"><pre>>>> t.add_row([-8, -9, 10])

>>> len(t)

4

</pre></div>

</div>

Lastly, one can create a table with support for missing values, for example by setting

<tt class="docutils literal">masked=True</tt>:

<div class="highlight-python"><div class="highlight"><pre>>>> t = Table([a, b, c], names=('a', 'b', 'c'), masked=True)

>>> t['a'].mask = [True, True, False]

>>> t

masked_array(data = [(--, 2.0, 'x') (--, 5.0, 'y') (5, 8.2, 'z')],

mask = [(True, False, False) (True, False, False) (False, False, False)],

fill_value = (999999, 1e+20, 'N'),

dtype = [('a', '<i8'), ('b', '<f8'), ('c', '|S1')])

>>> print(t)

a b c

--- --- ---

-- 2.0 x

-- 5.0 y

5 8.2 z

</pre></div>

</div>

Finally, every table can have meta-data attached to it via the <tt class="docutils literal">meta</tt>

attribute, which can be used like a Python dictionary:

<div class="highlight-python"><div class="highlight"><pre>>>> t.meta['creator'] = 'me'

</pre></div>

</div>

<h2>Reading and writing tables<a class="headerlink" href="#reading-and-writing-tables" title="Permalink to this headline">¶</a></h2>

<tt class="docutils literal">Table</tt> objects include <tt class="docutils literal">read</tt> and <tt class="docutils literal">write</tt> methods that can be used to

easily read and write the tables to different formats. The tutorial directory

contains a file named rosat.vot which is the ROSAT All-Sky Bright Source

Catalogue (1RXS) (Voges+ 1999) in the VO Table format.

You can read this in as a <tt class="docutils literal">Table</tt> object by simply doing:

</pre></div>

</div>

(just ignore the warnings, which are due to Vizier not complying with the VO

standard). We can see a quick overview of the table with:

<div class="highlight-python"><div class="highlight"><pre>>>> print(t)

_1RXS RAJ2000 DEJ2000 PosErr NewFlag Count e_Count HR1 e_HR1 HR2 e_HR2 Extent

---------------- --------- --------- ------ ------- --------- --------- ----- ----- ----- ----- ------

J000000.0-392902 0.00000 -39.48403 19 __.. 0.13 0.035 0.69 0.25 0.28 0.24 0

J000007.0+081653 0.02917 8.28153 10 TT.. 0.19 0.021 0.89 0.10 0.24 0.13 0

J000010.0-633543 0.04167 -63.59528 11 __.. 0.19 0.031 -0.36 0.13 -0.35 0.23 13

J000011.9+052318 0.04958 5.38833 7 __.. 0.26 0.026 0.24 0.10 0.00 0.13 0

J000012.6+014621 0.05250 1.77250 11 __.. 0.081 0.016 0.05 0.20 0.00 0.26 14

J000013.5+575628 0.05625 57.94125 8 __.. 0.12 0.017 0.57 0.12 0.32 0.14 0

J000019.5-261032 0.08125 -26.17556 12 __.. 0.12 0.022 -0.26 0.17 0.19 0.29 0

... ... ... ... ... ... ... ... ... ... ... ...

J235929.2-255851 359.87164 -25.98083 10 _T.. 0.23 0.028 -0.43 0.11 -0.30 0.26 13

J235929.3+334329 359.87207 33.72472 11 __.. 0.16 0.024 -0.62 0.12 -0.56 0.66 12

J235930.9-401541 359.87875 -40.26139 18 __.. 0.13 0.037 -0.73 0.18 0.02 0.82 0

J235940.9-314342 359.92041 -31.72847 19 __.. 0.058 0.017 0.17 0.30 0.33 0.34 0

J235941.2+830719 359.92166 83.12195 10 __.. 0.066 0.011 0.72 0.14 0.19 0.17 0

J235944.7+220014 359.93625 22.00389 17 __.. 0.052 0.015 -0.01 0.27 0.37 0.35 0

J235959.1+083355 359.99625 8.56528 10 __.. 0.12 0.018 0.54 0.13 0.10 0.17 9

</pre></div>

</div>

Since we are using IPython with the <tt class="docutils literal">--matplotlib</tt> option along with

<tt class="docutils literal">import matplotlib.pyplot as plt</tt>, we can easily make a

histogram of the count rates:

<div class="highlight-python"><div class="highlight"><pre>>>> plt.hist(t['Count'], range=[0., 2], bins=100)

</pre></div>

</div>

It is easy to select a subset of the table matching a given criterion:

<div class="highlight-python"><div class="highlight"><pre>>>> t_bright = t[t['Count'] > 0.2]

>>> len(t_bright)

3627

</pre></div>

</div>

Criteria can be combined:

<div class="highlight-python"><div class="highlight"><pre>>>> t_sub = t[(t['RAJ2000'] > 230.) & (t['RAJ2000'] < 260.) &

(t['DEJ2000'] > -60.) & (t['DEJ2000'] < -20)]

>>> len(t_sub)

642

</pre></div>

</div>

<h2>Practical Exercises<a class="headerlink" href="#practical-exercises" title="Permalink to this headline">¶</a></h2>

Excercise

Try and find a way to make a table of the ROSAT point source catalog that

contains only the RA, Dec, and count rate. Hint: you can see what methods

are available on an object by typing e.g. <tt class="docutils literal">t.</tt> and then pressing

<tt class="docutils literal"><TAB></tt>. You can also find help on a method by typing e.g.

<tt class="docutils literal">t.add_column?</tt>.

</div>

Click to Show/Hide Solution <div class="panel1"><div class="highlight-python"><div class="highlight"><pre>>>> t.keep_columns(['RAJ2000', 'DEJ2000', 'Count'])

>>> print(t)

RAJ2000 DEJ2000 Count

--------- --------- ---------

0.00000 -39.48403 0.13

0.02917 8.28153 0.19

0.04167 -63.59528 0.19

0.04958 5.38833 0.26

0.05250 1.77250 0.081

0.05625 57.94125 0.12

0.08125 -26.17556 0.12

... ... ...

359.87207 33.72472 0.16

359.87875 -40.26139 0.13

359.92041 -31.72847 0.058

359.92166 83.12195 0.066

359.93625 22.00389 0.052

359.99625 8.56528 0.12

Note that you can also do this with::

>>> t_new = t['RAJ2000', 'DEJ2000', 'Count']

>>> print(t_new)

RAJ2000 DEJ2000 Count

--------- --------- ---------

0.00000 -39.48403 0.13

0.02917 8.28153 0.19

0.04167 -63.59528 0.19

0.04958 5.38833 0.26

0.05250 1.77250 0.081

0.05625 57.94125 0.12

0.08125 -26.17556 0.12

... ... ...

359.87207 33.72472 0.16

359.87875 -40.26139 0.13

359.92041 -31.72847 0.058

359.92166 83.12195 0.066

359.93625 22.00389 0.052

359.99625 8.56528 0.12

</pre></div>

</div>

</div><div class="admonition-excercise-2 admonition">

Excercise 2

Make an all-sky equatorial plot of the ROSAT sources, with all sources

shown in black, and only the sources with a count rate larger than 2.

shown in red.

</div>

Click to Show/Hide Solution <div class="panel2"><div class="highlight-python"><div class="highlight"><pre>from astropy.table import Table

from matplotlib import pyplot as plt

t = Table.read('rosat.vot', format='votable')

t_bright = t[t['Count'] > 2.]

fig = plt.figure()

ax = fig.add_subplot(1,1,1, aspect='equal')

ax.scatter(t['RAJ2000'], t['DEJ2000'], s=1, color='black')

ax.scatter(t_bright['RAJ2000'], t_bright['DEJ2000'], color='red')

ax.set_xlim(360., 0.)

ax.set_ylim(-90., 90.)

ax.set_xlabel("Right Ascension")

ax.set_ylabel("Declination")

fig.savefig('tables_level2.png', bbox_inches='tight')

</pre></div>

</div>

</div><div class="admonition-excercise-3 admonition">

Excercise 3

Try and write out the ROSAT catalog into a format that you can read into

another software package (see <a class="reference external" href="http://docs.astropy.org/en/v0.2/table/io.html">here</a> for more details). For

example, try and write out the catalog into CSV format, then read it into

a spreadsheet software package (e.g. Excel, Google Docs, Numbers,

OpenOffice).

</div>

Click to Show/Hide Solution <div class="panel3">To write out the file:

<div class="highlight-python"><div class="highlight"><pre>>>> t.write('rosat2.csv', format='ascii', delimiter=',')

</pre></div>

</div>

Then you should be able to load it into another software package.

</div></div>

</div>

<div class="sphinxsidebarwrapper"><h3>Page Contents</h3>

<ul>

<li><a class="reference internal" href="#">Tabular data</a><ul>

<li><a class="reference internal" href="#documentation">Documentation</a></li>

<li><a class="reference internal" href="#constructing-and-manipulating-tables">Constructing and Manipulating tables</a></li>

<li><a class="reference internal" href="#reading-and-writing-tables">Reading and writing tables</a></li>

<li><a class="reference internal" href="#practical-exercises">Practical Exercises</a></li>

</ul>

</li>

</ul>

<h4>Previous topic</h4>

<a href="astropy.html"

title="previous chapter">Astropy I: core functions</a>

<h4>Next topic</h4>

<a href="fits.html"

title="next chapter">Handling FITS files</a>

</div>

</div>

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