From dfb at mrao.cam.ac.uk  Fri Mar  1 05:59:11 2013
From: dfb at mrao.cam.ac.uk (David Buscher)
Date: Fri, 1 Mar 2013 10:59:11 +0000
Subject: [AstroPy] Indexing table rows
Message-ID: <CA+UiVUwvjmOBqB7ra78WQY91TCQnJMPjfVeAs8b7F1q8A_No9g@mail.gmail.com>

It appears that the astropy.tables module does not accept the same row
indexing syntax as the corresponding ndarray, particularly the syntax
output by np.where(), which is a tuple containing an ndarray. Example
below:

Python 2.7.3 |EPD 7.3-1 (64-bit)| (default, Apr 12 2012, 11:14:05)
[GCC 4.0.1 (Apple Inc. build 5493)] on darwin
Type "credits", "demo" or "enthought" for more information.
>>> import numpy as np
>>> from astropy.table import Table

>>> t=Table(np.reshape(np.arange(12),(4,3)))
>>> print t
col0 col1 col2
---- ---- ----
   0    1    2
   3    4    5
   6    7    8
   9   10   11

>>> rows=np.where(t["col0"]>5)
>>> print rows
(array([2, 3]),)

# ndarray version
>>> print np.array(t)[rows]
[(6, 7, 8) (9, 10, 11)]

# Tables version
>>> print t[rows[0]]
col0 col1 col2
---- ---- ----
   6    7    8
   9   10   11

>>> print t[rows]
ERROR: TypeError: unhashable type: 'numpy.ndarray' [astropy.table.table]
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/astropy/table/table.py",
line 1282, in __getitem__
    if any(x not in set(self.colnames) for x in item):
  File "/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/astropy/table/table.py",
line 1282, in <genexpr>
    if any(x not in set(self.colnames) for x in item):
TypeError: unhashable type: 'numpy.ndarray'

I am using astropy version 0.2. Is this behaviour on purpose or a bug?
It can be worked around by taking the first element of the indexing
tuple as above, but it seems counterintuitive that the output of
np.where() cannot be used directly to select table rows.

David


From aldcroft at head.cfa.harvard.edu  Fri Mar  1 07:08:38 2013
From: aldcroft at head.cfa.harvard.edu (Tom Aldcroft)
Date: Fri, 1 Mar 2013 07:08:38 -0500
Subject: [AstroPy] Indexing table rows
In-Reply-To: <CA+UiVUwvjmOBqB7ra78WQY91TCQnJMPjfVeAs8b7F1q8A_No9g@mail.gmail.com>
References: <CA+UiVUwvjmOBqB7ra78WQY91TCQnJMPjfVeAs8b7F1q8A_No9g@mail.gmail.com>
Message-ID: <CAGsQ-NsH12=sKmsYNO5Gq0hz8kMFfsc_ZQudSW51Yx6K=O=hHA@mail.gmail.com>

Hi David,

Thanks for reporting this issue.  This is a bug and is now tracked at
  https://github.com/astropy/astropy/issues/838

This should be fixed in the 0.2.1 release scheduled for early April.

Cheers,
Tom

On Fri, Mar 1, 2013 at 5:59 AM, David Buscher <dfb at mrao.cam.ac.uk> wrote:
> It appears that the astropy.tables module does not accept the same row
> indexing syntax as the corresponding ndarray, particularly the syntax
> output by np.where(), which is a tuple containing an ndarray. Example
> below:
>
> Python 2.7.3 |EPD 7.3-1 (64-bit)| (default, Apr 12 2012, 11:14:05)
> [GCC 4.0.1 (Apple Inc. build 5493)] on darwin
> Type "credits", "demo" or "enthought" for more information.
>>>> import numpy as np
>>>> from astropy.table import Table
>
>>>> t=Table(np.reshape(np.arange(12),(4,3)))
>>>> print t
> col0 col1 col2
> ---- ---- ----
>    0    1    2
>    3    4    5
>    6    7    8
>    9   10   11
>
>>>> rows=np.where(t["col0"]>5)
>>>> print rows
> (array([2, 3]),)
>
> # ndarray version
>>>> print np.array(t)[rows]
> [(6, 7, 8) (9, 10, 11)]
>
> # Tables version
>>>> print t[rows[0]]
> col0 col1 col2
> ---- ---- ----
>    6    7    8
>    9   10   11
>
>>>> print t[rows]
> ERROR: TypeError: unhashable type: 'numpy.ndarray' [astropy.table.table]
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/astropy/table/table.py",
> line 1282, in __getitem__
>     if any(x not in set(self.colnames) for x in item):
>   File "/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/astropy/table/table.py",
> line 1282, in <genexpr>
>     if any(x not in set(self.colnames) for x in item):
> TypeError: unhashable type: 'numpy.ndarray'
>
> I am using astropy version 0.2. Is this behaviour on purpose or a bug?
> It can be worked around by taking the first element of the indexing
> tuple as above, but it seems counterintuitive that the output of
> np.where() cannot be used directly to select table rows.
>
> David
> _______________________________________________
> AstroPy mailing list
> AstroPy at scipy.org
> http://mail.scipy.org/mailman/listinfo/astropy
>


From aldcroft at head.cfa.harvard.edu  Fri Mar  1 07:56:27 2013
From: aldcroft at head.cfa.harvard.edu (Tom Aldcroft)
Date: Fri, 1 Mar 2013 07:56:27 -0500
Subject: [AstroPy] Indexing table rows
In-Reply-To: <CAGsQ-NsH12=sKmsYNO5Gq0hz8kMFfsc_ZQudSW51Yx6K=O=hHA@mail.gmail.com>
References: <CA+UiVUwvjmOBqB7ra78WQY91TCQnJMPjfVeAs8b7F1q8A_No9g@mail.gmail.com>
	<CAGsQ-NsH12=sKmsYNO5Gq0hz8kMFfsc_ZQudSW51Yx6K=O=hHA@mail.gmail.com>
Message-ID: <CAGsQ-NvyU54h1QWDGwMOk1Omc4Uw=PG+5m6yYOpGgoZrhydMdw@mail.gmail.com>

I forgot to mention that an alternate workaround is to use boolean masking:

>>> t = Table(np.reshape(np.arange(12),(4,3)))
>>> ok = t['col0'] > 5
>>> print t[ok]
col0 col1 col2
---- ---- ----
   6    7    8
   9   10   11

Cheers,
Tom

On Fri, Mar 1, 2013 at 7:08 AM, Tom Aldcroft
<aldcroft at head.cfa.harvard.edu> wrote:
> Hi David,
>
> Thanks for reporting this issue.  This is a bug and is now tracked at
>   https://github.com/astropy/astropy/issues/838
>
> This should be fixed in the 0.2.1 release scheduled for early April.
>
> Cheers,
> Tom
>
> On Fri, Mar 1, 2013 at 5:59 AM, David Buscher <dfb at mrao.cam.ac.uk> wrote:
>> It appears that the astropy.tables module does not accept the same row
>> indexing syntax as the corresponding ndarray, particularly the syntax
>> output by np.where(), which is a tuple containing an ndarray. Example
>> below:
>>
>> Python 2.7.3 |EPD 7.3-1 (64-bit)| (default, Apr 12 2012, 11:14:05)
>> [GCC 4.0.1 (Apple Inc. build 5493)] on darwin
>> Type "credits", "demo" or "enthought" for more information.
>>>>> import numpy as np
>>>>> from astropy.table import Table
>>
>>>>> t=Table(np.reshape(np.arange(12),(4,3)))
>>>>> print t
>> col0 col1 col2
>> ---- ---- ----
>>    0    1    2
>>    3    4    5
>>    6    7    8
>>    9   10   11
>>
>>>>> rows=np.where(t["col0"]>5)
>>>>> print rows
>> (array([2, 3]),)
>>
>> # ndarray version
>>>>> print np.array(t)[rows]
>> [(6, 7, 8) (9, 10, 11)]
>>
>> # Tables version
>>>>> print t[rows[0]]
>> col0 col1 col2
>> ---- ---- ----
>>    6    7    8
>>    9   10   11
>>
>>>>> print t[rows]
>> ERROR: TypeError: unhashable type: 'numpy.ndarray' [astropy.table.table]
>> Traceback (most recent call last):
>>   File "<stdin>", line 1, in <module>
>>   File "/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/astropy/table/table.py",
>> line 1282, in __getitem__
>>     if any(x not in set(self.colnames) for x in item):
>>   File "/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/astropy/table/table.py",
>> line 1282, in <genexpr>
>>     if any(x not in set(self.colnames) for x in item):
>> TypeError: unhashable type: 'numpy.ndarray'
>>
>> I am using astropy version 0.2. Is this behaviour on purpose or a bug?
>> It can be worked around by taking the first element of the indexing
>> tuple as above, but it seems counterintuitive that the output of
>> np.where() cannot be used directly to select table rows.
>>
>> David
>> _______________________________________________
>> AstroPy mailing list
>> AstroPy at scipy.org
>> http://mail.scipy.org/mailman/listinfo/astropy
>>


From dfb at mrao.cam.ac.uk  Fri Mar  1 09:06:45 2013
From: dfb at mrao.cam.ac.uk (David Buscher)
Date: Fri, 1 Mar 2013 14:06:45 +0000
Subject: [AstroPy] Indexing table rows
In-Reply-To: <CAGsQ-NvyU54h1QWDGwMOk1Omc4Uw=PG+5m6yYOpGgoZrhydMdw@mail.gmail.com>
References: <CA+UiVUwvjmOBqB7ra78WQY91TCQnJMPjfVeAs8b7F1q8A_No9g@mail.gmail.com>
	<CAGsQ-NsH12=sKmsYNO5Gq0hz8kMFfsc_ZQudSW51Yx6K=O=hHA@mail.gmail.com>
	<CAGsQ-NvyU54h1QWDGwMOk1Omc4Uw=PG+5m6yYOpGgoZrhydMdw@mail.gmail.com>
Message-ID: <CA+UiVUxwPop+2CjLig=GBUQ8S9iuAo1fp2-KyTDyOsgMxDV4zQ@mail.gmail.com>

Thanks for the quick response. In fact boolean indexing is a better
solution in my case, I just was not aware that I could do it...

David

On Fri, Mar 1, 2013 at 12:56 PM, Tom Aldcroft
<aldcroft at head.cfa.harvard.edu> wrote:
> I forgot to mention that an alternate workaround is to use boolean masking:
>
>>>> t = Table(np.reshape(np.arange(12),(4,3)))
>>>> ok = t['col0'] > 5
>>>> print t[ok]
> col0 col1 col2
> ---- ---- ----
>    6    7    8
>    9   10   11
>
> Cheers,
> Tom
>
> On Fri, Mar 1, 2013 at 7:08 AM, Tom Aldcroft
> <aldcroft at head.cfa.harvard.edu> wrote:
>> Hi David,
>>
>> Thanks for reporting this issue.  This is a bug and is now tracked at
>>   https://github.com/astropy/astropy/issues/838
>>
>> This should be fixed in the 0.2.1 release scheduled for early April.
>>
>> Cheers,
>> Tom
>>
>> On Fri, Mar 1, 2013 at 5:59 AM, David Buscher <dfb at mrao.cam.ac.uk> wrote:
>>> It appears that the astropy.tables module does not accept the same row
>>> indexing syntax as the corresponding ndarray, particularly the syntax
>>> output by np.where(), which is a tuple containing an ndarray. Example
>>> below:
>>>
>>> Python 2.7.3 |EPD 7.3-1 (64-bit)| (default, Apr 12 2012, 11:14:05)
>>> [GCC 4.0.1 (Apple Inc. build 5493)] on darwin
>>> Type "credits", "demo" or "enthought" for more information.
>>>>>> import numpy as np
>>>>>> from astropy.table import Table
>>>
>>>>>> t=Table(np.reshape(np.arange(12),(4,3)))
>>>>>> print t
>>> col0 col1 col2
>>> ---- ---- ----
>>>    0    1    2
>>>    3    4    5
>>>    6    7    8
>>>    9   10   11
>>>
>>>>>> rows=np.where(t["col0"]>5)
>>>>>> print rows
>>> (array([2, 3]),)
>>>
>>> # ndarray version
>>>>>> print np.array(t)[rows]
>>> [(6, 7, 8) (9, 10, 11)]
>>>
>>> # Tables version
>>>>>> print t[rows[0]]
>>> col0 col1 col2
>>> ---- ---- ----
>>>    6    7    8
>>>    9   10   11
>>>
>>>>>> print t[rows]
>>> ERROR: TypeError: unhashable type: 'numpy.ndarray' [astropy.table.table]
>>> Traceback (most recent call last):
>>>   File "<stdin>", line 1, in <module>
>>>   File "/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/astropy/table/table.py",
>>> line 1282, in __getitem__
>>>     if any(x not in set(self.colnames) for x in item):
>>>   File "/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/astropy/table/table.py",
>>> line 1282, in <genexpr>
>>>     if any(x not in set(self.colnames) for x in item):
>>> TypeError: unhashable type: 'numpy.ndarray'
>>>
>>> I am using astropy version 0.2. Is this behaviour on purpose or a bug?
>>> It can be worked around by taking the first element of the indexing
>>> tuple as above, but it seems counterintuitive that the output of
>>> np.where() cannot be used directly to select table rows.
>>>
>>> David
>>> _______________________________________________
>>> AstroPy mailing list
>>> AstroPy at scipy.org
>>> http://mail.scipy.org/mailman/listinfo/astropy
>>>


From jzuhone at gmail.com  Fri Mar  1 12:18:35 2013
From: jzuhone at gmail.com (John ZuHone)
Date: Fri, 1 Mar 2013 12:18:35 -0500
Subject: [AstroPy] Announcing the release of yt 2.5!
Message-ID: <3ED3883B-7B8D-4E07-8EA1-82791A4ED040@gmail.com>

Dear Colleagues,

We?re proud to announce the release of version 2.5 of the yt Project, http://yt-project.org/. The new version includes many new features, refinements of existing features and numerous bugfixes.  We encourage all users to upgrade to take advantage of the changes.

yt is a community-developed analysis and visualization toolkit, primarily directed at astrophysical hydrodynamics simulations.  It provides full support for output from the Enzo, FLASH, Orion, and Nyx codes, with preliminary support for several others.  It provides access to simulation data using an intuitive python interface, can perform many common visualization tasks, and offers a framework for conducting data reductions and analysis of simulation data.

The most visible changes with the 2.5 release include:

* Testing has been greatly expanded, including unit tests and answer testing. 
* The capabilities of the ?Stream? frontend have been expanded. Uniform grid and AMR-based data can be read into memory, and particle fields can be initialized. 
* The install script now provides for the optional installation of SciPy and the Rockstar halo finder. 
* Surfaces can now be extracted and examined, as well as uploaded to Sketchfab.com for interactive visualization in a web browser.
* Support for the Athena code has been added. 
* Many, many improvements to PlotWindow.
* Coordinate transformations have been sped up and streamlined, as well as cylindrical and spherical fields.
* Increased support for the IPython notebook. 
* Improved support for FLASH particle fields. 
* The volume rendering backend has been updated to use an alpha channel, fixing parallel opaque volume renderings.
* The AMRKDTree has been rewritten, allowing parallelism with other than power-of-2 MPI processes, arbitrary sets of grids, and splitting of unigrids.

For a complete list of changes in this release, please visit the Changelog (http://yt-project.org/docs/2.5/changelog.html).

Information about the yt project, including installation instructions, can be found on the homepage: http://yt-project.org/

Development of yt has been sponsored by the NSF, the DOE, and various universities.  We develop yt in the open and encourage contributions from users who extend and improve the code.  We invite you to get involved with developing and using yt!

Please forward this announcement to other interested parties.

Sincerely,

The yt development team



From susanasanche at gmail.com  Mon Mar  4 06:43:20 2013
From: susanasanche at gmail.com (Susana Sanchez)
Date: Mon, 4 Mar 2013 12:43:20 +0100
Subject: [AstroPy] How can I create a VOtable from a python list?
Message-ID: <CAK=du8L+A8wyijjVsGzj4h9hueTLxf9hsyiwGdYZYGuEgniKEQ@mail.gmail.com>

Hello all,

How can I create a VOtable from a list (a python list) of rows using astropy?

Reading the documentation, I found the method "from_table" of the
class VOTableFile, this method needs as argument an instance of the
class astropy.table.table.Table, so I did the following:

t=astropy.table.table.Table([["CIG12",1.2345,0,2,999,"COMMENT"],["CIG122",1.23452,0,2,9992,"COMMENT2"]])
votable = VOTableFile()
votable.from_table(t)


But here I got this error:

/usr/local/lib/python2.6/dist-packages/numpy/ma/core.pyc in
__new__(cls, data, mask, dtype, copy, subok, ndmin, fill_value,
keep_mask, hard_mask, shrink, **options)
   2692             # Or assume it's a sequence of bool/int

   2693             except TypeError:
-> 2694                 mask = np.array([tuple([m] * len(mdtype)) for
m in mask],
   2695                                  dtype=mdtype)
   2696             # Make sure the mask and the data have the same shape

TypeError: 'NoneType' object is not iterable


Reading the error message,  I thought it could be related with the
mask, so I tried to create the mask of the table t (with the method
t.create_mask()), and then to build the VOTableFile from this table,
but I got the same error.

I would be very gratefully, If anyone can help me or give me any hint.

Thanks,
Susana.


From mdroe at stsci.edu  Wed Mar  6 09:08:41 2013
From: mdroe at stsci.edu (Michael Droettboom)
Date: Wed, 6 Mar 2013 09:08:41 -0500
Subject: [AstroPy] How can I create a VOtable from a python list?
In-Reply-To: <CAK=du8L+A8wyijjVsGzj4h9hueTLxf9hsyiwGdYZYGuEgniKEQ@mail.gmail.com>
References: <CAK=du8L+A8wyijjVsGzj4h9hueTLxf9hsyiwGdYZYGuEgniKEQ@mail.gmail.com>
Message-ID: <51374DE9.5050006@stsci.edu>

The general approach you're taking here -- to create a Table and then 
convert it to a VOTable -- is the right one here.  The Table class has a 
much richer set of things it can convert to and from (it's sort of our 
"hub" class for everything that's table like).

However, I don't believe it supports construction from a list in the way 
you're trying.  There is a doc page about constructing a table here, 
that may be helpful:

https://astropy.readthedocs.org/en/v0.2/table/construct_table.html

That said, I tried to convert your example to the form where the Table 
is constructed from a Numpy structured array, and still ran into the 
same exception:

from astropy import table

from astropy.io import votable

import numpy as np

x = np.array(

     [("CIG12",1.2345,0,2,999,"COMMENT"),

      ("CIG122",1.23452,0,2,9992,"COMMENT2")],

     dtype=[('a', str), ('b', float), ('c', int), ('d', int), ('e', int), ('f', str)])

print x.dtype

t = table.Table(x)

votable = votable.tree.VOTableFile.from_table(t)


So maybe we're both still doing something wrong.  I've Cc'd Tom 
Aldcroft, the primary author of the Table class, as he might have more 
insight.

Mike


On 03/04/2013 06:43 AM, Susana Sanchez wrote:
> Hello all,
>
> How can I create a VOtable from a list (a python list) of rows using astropy?
>
> Reading the documentation, I found the method "from_table" of the
> class VOTableFile, this method needs as argument an instance of the
> class astropy.table.table.Table, so I did the following:
>
> t=astropy.table.table.Table([["CIG12",1.2345,0,2,999,"COMMENT"],["CIG122",1.23452,0,2,9992,"COMMENT2"]])
> votable = VOTableFile()
> votable.from_table(t)
>
>
> But here I got this error:
>
> /usr/local/lib/python2.6/dist-packages/numpy/ma/core.pyc in
> __new__(cls, data, mask, dtype, copy, subok, ndmin, fill_value,
> keep_mask, hard_mask, shrink, **options)
>     2692             # Or assume it's a sequence of bool/int
>
>     2693             except TypeError:
> -> 2694                 mask = np.array([tuple([m] * len(mdtype)) for
> m in mask],
>     2695                                  dtype=mdtype)
>     2696             # Make sure the mask and the data have the same shape
>
> TypeError: 'NoneType' object is not iterable
>
>
> Reading the error message,  I thought it could be related with the
> mask, so I tried to create the mask of the table t (with the method
> t.create_mask()), and then to build the VOTableFile from this table,
> but I got the same error.
>
> I would be very gratefully, If anyone can help me or give me any hint.
>
> Thanks,
> Susana.
> _______________________________________________
> AstroPy mailing list
> AstroPy at scipy.org
> http://mail.scipy.org/mailman/listinfo/astropy



From marquett at iap.fr  Wed Mar  6 09:28:44 2013
From: marquett at iap.fr (Jean-Baptiste Marquette)
Date: Wed, 6 Mar 2013 15:28:44 +0100
Subject: [AstroPy] How can I create a VOtable from a python list?
In-Reply-To: <51374DE9.5050006@stsci.edu>
References: <CAK=du8L+A8wyijjVsGzj4h9hueTLxf9hsyiwGdYZYGuEgniKEQ@mail.gmail.com>
	<51374DE9.5050006@stsci.edu>
Message-ID: <1B5131CB-E186-4C5B-B5AF-29263BE54EC0@iap.fr>

Hi all,

May I suggest to have a look at ATpy, where VOTable are natively recognized: http://atpy.github.com/ ?

BTW, I would be very grateful if both AstroPy and ATpy could merge?

Cheers,
Jean-Baptiste

Le 6 mars 2013 ? 15:08, Michael Droettboom a ?crit :

> The general approach you're taking here -- to create a Table and then 
> convert it to a VOTable -- is the right one here.  The Table class has a 
> much richer set of things it can convert to and from (it's sort of our 
> "hub" class for everything that's table like).
> 
> However, I don't believe it supports construction from a list in the way 
> you're trying.  There is a doc page about constructing a table here, 
> that may be helpful:
> 
> https://astropy.readthedocs.org/en/v0.2/table/construct_table.html
> 
> That said, I tried to convert your example to the form where the Table 
> is constructed from a Numpy structured array, and still ran into the 
> same exception:
> 
> from astropy import table
> 
> from astropy.io import votable
> 
> import numpy as np
> 
> x = np.array(
> 
>     [("CIG12",1.2345,0,2,999,"COMMENT"),
> 
>      ("CIG122",1.23452,0,2,9992,"COMMENT2")],
> 
>     dtype=[('a', str), ('b', float), ('c', int), ('d', int), ('e', int), ('f', str)])
> 
> print x.dtype
> 
> t = table.Table(x)
> 
> votable = votable.tree.VOTableFile.from_table(t)
> 
> 
> So maybe we're both still doing something wrong.  I've Cc'd Tom 
> Aldcroft, the primary author of the Table class, as he might have more 
> insight.
> 
> Mike
> 
> 
> On 03/04/2013 06:43 AM, Susana Sanchez wrote:
>> Hello all,
>> 
>> How can I create a VOtable from a list (a python list) of rows using astropy?
>> 
>> Reading the documentation, I found the method "from_table" of the
>> class VOTableFile, this method needs as argument an instance of the
>> class astropy.table.table.Table, so I did the following:
>> 
>> t=astropy.table.table.Table([["CIG12",1.2345,0,2,999,"COMMENT"],["CIG122",1.23452,0,2,9992,"COMMENT2"]])
>> votable = VOTableFile()
>> votable.from_table(t)
>> 
>> 
>> But here I got this error:
>> 
>> /usr/local/lib/python2.6/dist-packages/numpy/ma/core.pyc in
>> __new__(cls, data, mask, dtype, copy, subok, ndmin, fill_value,
>> keep_mask, hard_mask, shrink, **options)
>>    2692             # Or assume it's a sequence of bool/int
>> 
>>    2693             except TypeError:
>> -> 2694                 mask = np.array([tuple([m] * len(mdtype)) for
>> m in mask],
>>    2695                                  dtype=mdtype)
>>    2696             # Make sure the mask and the data have the same shape
>> 
>> TypeError: 'NoneType' object is not iterable
>> 
>> 
>> Reading the error message,  I thought it could be related with the
>> mask, so I tried to create the mask of the table t (with the method
>> t.create_mask()), and then to build the VOTableFile from this table,
>> but I got the same error.
>> 
>> I would be very gratefully, If anyone can help me or give me any hint.
>> 
>> Thanks,
>> Susana.
>> _______________________________________________
>> AstroPy mailing list
>> AstroPy at scipy.org
>> http://mail.scipy.org/mailman/listinfo/astropy
> 
> _______________________________________________
> AstroPy mailing list
> AstroPy at scipy.org
> http://mail.scipy.org/mailman/listinfo/astropy

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From thomas.robitaille at gmail.com  Wed Mar  6 10:57:10 2013
From: thomas.robitaille at gmail.com (Thomas Robitaille)
Date: Wed, 6 Mar 2013 16:57:10 +0100
Subject: [AstroPy] How can I create a VOtable from a python list?
In-Reply-To: <1B5131CB-E186-4C5B-B5AF-29263BE54EC0@iap.fr>
References: <CAK=du8L+A8wyijjVsGzj4h9hueTLxf9hsyiwGdYZYGuEgniKEQ@mail.gmail.com>
	<51374DE9.5050006@stsci.edu>
	<1B5131CB-E186-4C5B-B5AF-29263BE54EC0@iap.fr>
Message-ID: <CAGMHX_10-7cr-yB41Hy2DjEvVWGtj81HmOQ0b6D-WSTegLG-Xg@mail.gmail.com>

Hi Jean-Baptiste,

Astropy actually already supports the same kind of file access to VO
tables that ATpy does - if you have an Astropy Table object, you can
do:

t = Table(...)
t.write('my_table.xml', format='votable')

to read a VO table:

t = Table.read('my_table.xml')

(format should be auto-detected)

We've been working on merging the ATpy functionality bit by bit (in
fact astropy.table started from the base Table class in ATpy). Astropy
can now be used as a full replacement to ATpy for VO tables, HDF5
tables, and ASCII tables. We will add support for FITS files, which
leaves only the SQL as being ATpy-specific (whether this gets merged
in future into Astropy remains to be decided).

Cheers,
Tom


On 6 March 2013 15:28, Jean-Baptiste Marquette <marquett at iap.fr> wrote:
> Hi all,
>
> May I suggest to have a look at ATpy, where VOTable are natively recognized:
> http://atpy.github.com/ ?
>
> BTW, I would be very grateful if both AstroPy and ATpy could merge?
>
> Cheers,
> Jean-Baptiste
>
> Le 6 mars 2013 ? 15:08, Michael Droettboom a ?crit :
>
> The general approach you're taking here -- to create a Table and then
> convert it to a VOTable -- is the right one here.  The Table class has a
> much richer set of things it can convert to and from (it's sort of our
> "hub" class for everything that's table like).
>
> However, I don't believe it supports construction from a list in the way
> you're trying.  There is a doc page about constructing a table here,
> that may be helpful:
>
> https://astropy.readthedocs.org/en/v0.2/table/construct_table.html
>
> That said, I tried to convert your example to the form where the Table
> is constructed from a Numpy structured array, and still ran into the
> same exception:
>
> from astropy import table
>
> from astropy.io import votable
>
> import numpy as np
>
> x = np.array(
>
>     [("CIG12",1.2345,0,2,999,"COMMENT"),
>
>      ("CIG122",1.23452,0,2,9992,"COMMENT2")],
>
>     dtype=[('a', str), ('b', float), ('c', int), ('d', int), ('e', int),
> ('f', str)])
>
> print x.dtype
>
> t = table.Table(x)
>
> votable = votable.tree.VOTableFile.from_table(t)
>
>
> So maybe we're both still doing something wrong.  I've Cc'd Tom
> Aldcroft, the primary author of the Table class, as he might have more
> insight.
>
> Mike
>
>
> On 03/04/2013 06:43 AM, Susana Sanchez wrote:
>
> Hello all,
>
>
> How can I create a VOtable from a list (a python list) of rows using
> astropy?
>
>
> Reading the documentation, I found the method "from_table" of the
>
> class VOTableFile, this method needs as argument an instance of the
>
> class astropy.table.table.Table, so I did the following:
>
>
> t=astropy.table.table.Table([["CIG12",1.2345,0,2,999,"COMMENT"],["CIG122",1.23452,0,2,9992,"COMMENT2"]])
>
> votable = VOTableFile()
>
> votable.from_table(t)
>
>
>
> But here I got this error:
>
>
> /usr/local/lib/python2.6/dist-packages/numpy/ma/core.pyc in
>
> __new__(cls, data, mask, dtype, copy, subok, ndmin, fill_value,
>
> keep_mask, hard_mask, shrink, **options)
>
>    2692             # Or assume it's a sequence of bool/int
>
>
>    2693             except TypeError:
>
> -> 2694                 mask = np.array([tuple([m] * len(mdtype)) for
>
> m in mask],
>
>    2695                                  dtype=mdtype)
>
>    2696             # Make sure the mask and the data have the same shape
>
>
> TypeError: 'NoneType' object is not iterable
>
>
>
> Reading the error message,  I thought it could be related with the
>
> mask, so I tried to create the mask of the table t (with the method
>
> t.create_mask()), and then to build the VOTableFile from this table,
>
> but I got the same error.
>
>
> I would be very gratefully, If anyone can help me or give me any hint.
>
>
> Thanks,
>
> Susana.
>
> _______________________________________________
>
> AstroPy mailing list
>
> AstroPy at scipy.org
>
> http://mail.scipy.org/mailman/listinfo/astropy
>
>
> _______________________________________________
> AstroPy mailing list
> AstroPy at scipy.org
> http://mail.scipy.org/mailman/listinfo/astropy
>
>
>
> _______________________________________________
> AstroPy mailing list
> AstroPy at scipy.org
> http://mail.scipy.org/mailman/listinfo/astropy
>


From thomas.robitaille at gmail.com  Wed Mar  6 11:03:53 2013
From: thomas.robitaille at gmail.com (Thomas Robitaille)
Date: Wed, 6 Mar 2013 17:03:53 +0100
Subject: [AstroPy] How can I create a VOtable from a python list?
In-Reply-To: <51374DE9.5050006@stsci.edu>
References: <CAK=du8L+A8wyijjVsGzj4h9hueTLxf9hsyiwGdYZYGuEgniKEQ@mail.gmail.com>
	<51374DE9.5050006@stsci.edu>
Message-ID: <CAGMHX_0_Nn6vhiLz11YufF27+LK1Tm8GiytvjAzf8QnWOxp4fw@mail.gmail.com>

Hi Susana and Mike,

This looks like a bug to me - I've opened
https://github.com/astropy/astropy/issues/849

Also, initializing from a list of tuples currently behaves the same as
a list of lists:

In [11]: t = Table([("CIG12",1.2345,0,2,999,"COMMENT"),("CIG122",1.23452,0,2,9992,"COMMENT2")])

In [12]: print(t)
  col0    col1
------- --------
  CIG12   CIG122
 1.2345  1.23452
      0        0
      2        2
    999     9992
COMMENT COMMENT2

but I think that to be consistent with Numpy, initializing from a list
of tuples should create tables with each tuple being a row, which is
what Susana wanted to do. Initializing from a list of lists should
treat them as columns, as it does.

Cheers,
Tom


On 6 March 2013 15:08, Michael Droettboom <mdroe at stsci.edu> wrote:
> The general approach you're taking here -- to create a Table and then
> convert it to a VOTable -- is the right one here.  The Table class has a
> much richer set of things it can convert to and from (it's sort of our
> "hub" class for everything that's table like).
>
> However, I don't believe it supports construction from a list in the way
> you're trying.  There is a doc page about constructing a table here,
> that may be helpful:
>
> https://astropy.readthedocs.org/en/v0.2/table/construct_table.html
>
> That said, I tried to convert your example to the form where the Table
> is constructed from a Numpy structured array, and still ran into the
> same exception:
>
> from astropy import table
>
> from astropy.io import votable
>
> import numpy as np
>
> x = np.array(
>
>      [("CIG12",1.2345,0,2,999,"COMMENT"),
>
>       ("CIG122",1.23452,0,2,9992,"COMMENT2")],
>
>      dtype=[('a', str), ('b', float), ('c', int), ('d', int), ('e', int), ('f', str)])
>
> print x.dtype
>
> t = table.Table(x)
>
> votable = votable.tree.VOTableFile.from_table(t)
>
>
> So maybe we're both still doing something wrong.  I've Cc'd Tom
> Aldcroft, the primary author of the Table class, as he might have more
> insight.
>
> Mike
>
>
> On 03/04/2013 06:43 AM, Susana Sanchez wrote:
>> Hello all,
>>
>> How can I create a VOtable from a list (a python list) of rows using astropy?
>>
>> Reading the documentation, I found the method "from_table" of the
>> class VOTableFile, this method needs as argument an instance of the
>> class astropy.table.table.Table, so I did the following:
>>
>> t=astropy.table.table.Table([["CIG12",1.2345,0,2,999,"COMMENT"],["CIG122",1.23452,0,2,9992,"COMMENT2"]])
>> votable = VOTableFile()
>> votable.from_table(t)
>>
>>
>> But here I got this error:
>>
>> /usr/local/lib/python2.6/dist-packages/numpy/ma/core.pyc in
>> __new__(cls, data, mask, dtype, copy, subok, ndmin, fill_value,
>> keep_mask, hard_mask, shrink, **options)
>>     2692             # Or assume it's a sequence of bool/int
>>
>>     2693             except TypeError:
>> -> 2694                 mask = np.array([tuple([m] * len(mdtype)) for
>> m in mask],
>>     2695                                  dtype=mdtype)
>>     2696             # Make sure the mask and the data have the same shape
>>
>> TypeError: 'NoneType' object is not iterable
>>
>>
>> Reading the error message,  I thought it could be related with the
>> mask, so I tried to create the mask of the table t (with the method
>> t.create_mask()), and then to build the VOTableFile from this table,
>> but I got the same error.
>>
>> I would be very gratefully, If anyone can help me or give me any hint.
>>
>> Thanks,
>> Susana.
>> _______________________________________________
>> AstroPy mailing list
>> AstroPy at scipy.org
>> http://mail.scipy.org/mailman/listinfo/astropy
>
> _______________________________________________
> AstroPy mailing list
> AstroPy at scipy.org
> http://mail.scipy.org/mailman/listinfo/astropy


From marquett at iap.fr  Wed Mar  6 11:05:31 2013
From: marquett at iap.fr (Jean-Baptiste Marquette)
Date: Wed, 6 Mar 2013 17:05:31 +0100
Subject: [AstroPy] How can I create a VOtable from a python list?
In-Reply-To: <CAGMHX_10-7cr-yB41Hy2DjEvVWGtj81HmOQ0b6D-WSTegLG-Xg@mail.gmail.com>
References: <CAK=du8L+A8wyijjVsGzj4h9hueTLxf9hsyiwGdYZYGuEgniKEQ@mail.gmail.com>
	<51374DE9.5050006@stsci.edu>
	<1B5131CB-E186-4C5B-B5AF-29263BE54EC0@iap.fr>
	<CAGMHX_10-7cr-yB41Hy2DjEvVWGtj81HmOQ0b6D-WSTegLG-Xg@mail.gmail.com>
Message-ID: <ECDB1BEB-F9B5-46FE-8291-F4AA5642084C@iap.fr>


Hi Tom,

> Astropy actually already supports the same kind of file access to VO
> tables that ATpy does - if you have an Astropy Table object, you can
> do:
> 
> t = Table(...)
> t.write('my_table.xml', format='votable')
> 
> to read a VO table:
> 
> t = Table.read('my_table.xml')
> 
> (format should be auto-detected)
> 
> We've been working on merging the ATpy functionality bit by bit (in
> fact astropy.table started from the base Table class in ATpy). Astropy
> can now be used as a full replacement to ATpy for VO tables, HDF5
> tables, and ASCII tables. We will add support for FITS files, which
> leaves only the SQL as being ATpy-specific (whether this gets merged
> in future into Astropy remains to be decided).

Excellent news! I just implemented in my scripts some other functionalities from Astropy dealing with WCS and FITS, I must say this is really awesome?

Cheers,
JB
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From aldcroft at head.cfa.harvard.edu  Wed Mar  6 11:07:11 2013
From: aldcroft at head.cfa.harvard.edu (Tom Aldcroft)
Date: Wed, 6 Mar 2013 11:07:11 -0500
Subject: [AstroPy] How can I create a VOtable from a python list?
In-Reply-To: <51374DE9.5050006@stsci.edu>
References: <CAK=du8L+A8wyijjVsGzj4h9hueTLxf9hsyiwGdYZYGuEgniKEQ@mail.gmail.com>
	<51374DE9.5050006@stsci.edu>
Message-ID: <CAGsQ-NtP2J8-uQ7dQNPbX48Chi2V0BZ=coydNhUiXKVH=m-Tug@mail.gmail.com>

Sorry for the delay.  For Susana, the hitch here is that you are
supplying data as a list of data rows, but Table requires input as a
list of data columns.  The easiest way (I know) to get around this is
to use np.rec.fromrecords:

>>> dat_rows = [["CIG12",1.2345,0,2,999,"COMMENT"],["CIG122",1.23452,0,2,9992,"COMMENT2"]]
>>> dat_np = np.rec.fromrecords(dat_rows)  # can also supply names=['col1', ...] for col names
>>> dat = Table(dat_np)

Referring to Tom Robitaille's later comment, I don't think this is a
bug, but we can discuss in the new issue thread.  More on that later.

- Tom

On Wed, Mar 6, 2013 at 9:08 AM, Michael Droettboom <mdroe at stsci.edu> wrote:
> The general approach you're taking here -- to create a Table and then
> convert it to a VOTable -- is the right one here.  The Table class has a
> much richer set of things it can convert to and from (it's sort of our "hub"
> class for everything that's table like).
>
> However, I don't believe it supports construction from a list in the way
> you're trying.  There is a doc page about constructing a table here, that
> may be helpful:
>
> https://astropy.readthedocs.org/en/v0.2/table/construct_table.html
>
> That said, I tried to convert your example to the form where the Table is
> constructed from a Numpy structured array, and still ran into the same
> exception:
>
> from astropy import table
>
> from astropy.io import votable
>
> import numpy as np
>
> x = np.array(
>
>     [("CIG12",1.2345,0,2,999,"COMMENT"),
>
>      ("CIG122",1.23452,0,2,9992,"COMMENT2")],
>
>     dtype=[('a', str), ('b', float), ('c', int), ('d', int), ('e', int),
> ('f', str)])
>
> print x.dtype
>
> t = table.Table(x)
>
> votable = votable.tree.VOTableFile.from_table(t)
>
>
> So maybe we're both still doing something wrong.  I've Cc'd Tom Aldcroft,
> the primary author of the Table class, as he might have more insight.
>
> Mike
>
>
>
> On 03/04/2013 06:43 AM, Susana Sanchez wrote:
>>
>> Hello all,
>>
>> How can I create a VOtable from a list (a python list) of rows using
>> astropy?
>>
>> Reading the documentation, I found the method "from_table" of the
>> class VOTableFile, this method needs as argument an instance of the
>> class astropy.table.table.Table, so I did the following:
>>
>>
>> t=astropy.table.table.Table([["CIG12",1.2345,0,2,999,"COMMENT"],["CIG122",1.23452,0,2,9992,"COMMENT2"]])
>> votable = VOTableFile()
>> votable.from_table(t)
>>
>>
>> But here I got this error:
>>
>> /usr/local/lib/python2.6/dist-packages/numpy/ma/core.pyc in
>> __new__(cls, data, mask, dtype, copy, subok, ndmin, fill_value,
>> keep_mask, hard_mask, shrink, **options)
>>     2692             # Or assume it's a sequence of bool/int
>>
>>     2693             except TypeError:
>> -> 2694                 mask = np.array([tuple([m] * len(mdtype)) for
>> m in mask],
>>     2695                                  dtype=mdtype)
>>     2696             # Make sure the mask and the data have the same shape
>>
>> TypeError: 'NoneType' object is not iterable
>>
>>
>> Reading the error message,  I thought it could be related with the
>> mask, so I tried to create the mask of the table t (with the method
>> t.create_mask()), and then to build the VOTableFile from this table,
>> but I got the same error.
>>
>> I would be very gratefully, If anyone can help me or give me any hint.
>>
>> Thanks,
>> Susana.
>> _______________________________________________
>> AstroPy mailing list
>> AstroPy at scipy.org
>> http://mail.scipy.org/mailman/listinfo/astropy
>
>


From sse at iaa.es  Wed Mar  6 11:19:38 2013
From: sse at iaa.es (Susana Sanchez Exposito)
Date: Wed, 6 Mar 2013 17:19:38 +0100
Subject: [AstroPy] How can I create a VOtable from a python list?
In-Reply-To: <51374DE9.5050006@stsci.edu>
References: <CAK=du8L+A8wyijjVsGzj4h9hueTLxf9hsyiwGdYZYGuEgniKEQ@mail.gmail.com>
	<51374DE9.5050006@stsci.edu>
Message-ID: <CAK=du8J2KYTJs_NUZNtLddkn6kqTn0r5BYEssNVP56PZgGTZ6A@mail.gmail.com>

Hi all and thanks for the answers,

I realized in
/usr/local/lib/python2.6/dist-packages/astropy/io/votable/tree.py the
way to pass the mask in the line 2672 is :

new_table.array = ma.array(np.asarray(table), mask=table.mask)

If you change this line for this:
new_table.array = ma.array(np.asarray(table), mask=ma.getmaskarray(table))

The error disappears. But then, when you try to save the table in a
xml file with votable.to_xml("table.xml"), you get this error:
/usr/local/lib/python2.6/dist-packages/astropy/utils/xml/writer.pyc in
xml_escape_cdata(s)
     14     Escapes &, < and > in an XML CDATA string.
     15     """
---> 16     s = s.replace(u"&", u"&amp;")
     17     s = s.replace(u"<", u"&lt;")
     18     s = s.replace(u">", u"&gt;")

UnicodeDecodeError: 'ascii' codec can't decode byte 0x8d in position
0: ordinal not in range(128)



Susana.



2013/3/6 Michael Droettboom <mdroe at stsci.edu>:
> The general approach you're taking here -- to create a Table and then
> convert it to a VOTable -- is the right one here.  The Table class has a
> much richer set of things it can convert to and from (it's sort of our
> "hub" class for everything that's table like).
>
> However, I don't believe it supports construction from a list in the way
> you're trying.  There is a doc page about constructing a table here,
> that may be helpful:
>
> https://astropy.readthedocs.org/en/v0.2/table/construct_table.html
>
> That said, I tried to convert your example to the form where the Table
> is constructed from a Numpy structured array, and still ran into the
> same exception:
>
> from astropy import table
>
> from astropy.io import votable
>
> import numpy as np
>
> x = np.array(
>
>      [("CIG12",1.2345,0,2,999,"COMMENT"),
>
>       ("CIG122",1.23452,0,2,9992,"COMMENT2")],
>
>      dtype=[('a', str), ('b', float), ('c', int), ('d', int), ('e', int), ('f', str)])
>
> print x.dtype
>
> t = table.Table(x)
>
> votable = votable.tree.VOTableFile.from_table(t)
>
>
> So maybe we're both still doing something wrong.  I've Cc'd Tom
> Aldcroft, the primary author of the Table class, as he might have more
> insight.
>
> Mike
>
>
> On 03/04/2013 06:43 AM, Susana Sanchez wrote:
>> Hello all,
>>
>> How can I create a VOtable from a list (a python list) of rows using astropy?
>>
>> Reading the documentation, I found the method "from_table" of the
>> class VOTableFile, this method needs as argument an instance of the
>> class astropy.table.table.Table, so I did the following:
>>
>> t=astropy.table.table.Table([["CIG12",1.2345,0,2,999,"COMMENT"],["CIG122",1.23452,0,2,9992,"COMMENT2"]])
>> votable = VOTableFile()
>> votable.from_table(t)
>>
>>
>> But here I got this error:
>>
>> /usr/local/lib/python2.6/dist-packages/numpy/ma/core.pyc in
>> __new__(cls, data, mask, dtype, copy, subok, ndmin, fill_value,
>> keep_mask, hard_mask, shrink, **options)
>>     2692             # Or assume it's a sequence of bool/int
>>
>>     2693             except TypeError:
>> -> 2694                 mask = np.array([tuple([m] * len(mdtype)) for
>> m in mask],
>>     2695                                  dtype=mdtype)
>>     2696             # Make sure the mask and the data have the same shape
>>
>> TypeError: 'NoneType' object is not iterable
>>
>>
>> Reading the error message,  I thought it could be related with the
>> mask, so I tried to create the mask of the table t (with the method
>> t.create_mask()), and then to build the VOTableFile from this table,
>> but I got the same error.
>>
>> I would be very gratefully, If anyone can help me or give me any hint.
>>
>> Thanks,
>> Susana.
>> _______________________________________________
>> AstroPy mailing list
>> AstroPy at scipy.org
>> http://mail.scipy.org/mailman/listinfo/astropy
>
> _______________________________________________
> AstroPy mailing list
> AstroPy at scipy.org
> http://mail.scipy.org/mailman/listinfo/astropy



-- 
Susana S?nchez Exp?sito

Instituto de Astrof?sica de Andaluc?a   IAA (CSIC)
Camino Bajo de Hu?tor, 50. Granada E-18008
Tel:(+34) 958 121 311 / (+34) 958 230 618
Fax:(+34) 958 814 530
e-mail: sse at iaa.es


From sse at iaa.es  Thu Mar  7 06:33:08 2013
From: sse at iaa.es (Susana Sanchez Exposito)
Date: Thu, 7 Mar 2013 12:33:08 +0100
Subject: [AstroPy] How can I preserve the precision of the data in the
	votable file?
Message-ID: <CAK=du8+82vyGD1FpTYu6Tc=Rj4YKLfv7ksnzRL3M6_YKUK_pVw@mail.gmail.com>

Hello again,

I have followed the instructions given by Tom Aldcroft as answer of my
previous mail (thanks for that!), and finally I get the xml file with
the VOTable, but I realized the number are rounded when they are
written in the xml file.

For example, if I have a table like this:
(I built this Table following the example in
https://astropy.readthedocs.org/en/v0.2/io/votable/index.html,
"Building a new table from scratch"):

In [62]: table
Out[62]: <astropy.io.votable.tree.Table object at 0x32bcbd0>

In [63]: table.array
Out[63]:
masked_rec.array(data = [(17.257360147629999, 18.999976544568401)
 (13.257360147629999, 78.999976544568398)],
                 mask = [(False, False) (False, False)],
           fill_value = (1e+20, 1e+20),
                dtype = [('precision', '<f8'), ('precision2', '<f8')])


When I build the xml file with the comand votable.to_xml, the file
contains this data:

 <TABLEDATA>
     <TR>
      <TD>17.2574</TD>
      <TD>19</TD>
     </TR>
     <TR>
      <TD>13.2574</TD>
      <TD>79</TD>
     </TR>
    </TABLEDATA>


As you can see, the numbers have been rounded, but I would like to
preserve the precision of these data. Is this possible?


Thanks again for your useful help!

Susana.
-- 
Susana S?nchez Exp?sito

Instituto de Astrof?sica de Andaluc?a   IAA (CSIC)
Camino Bajo de Hu?tor, 50. Granada E-18008
Tel:(+34) 958 121 311 / (+34) 958 230 618
Fax:(+34) 958 814 530
e-mail: sse at iaa.es


From mdroe at stsci.edu  Thu Mar  7 11:12:11 2013
From: mdroe at stsci.edu (Michael Droettboom)
Date: Thu, 7 Mar 2013 11:12:11 -0500
Subject: [AstroPy] How can I preserve the precision of the data in the
 votable file?
In-Reply-To: <CAK=du8+82vyGD1FpTYu6Tc=Rj4YKLfv7ksnzRL3M6_YKUK_pVw@mail.gmail.com>
References: <CAK=du8+82vyGD1FpTYu6Tc=Rj4YKLfv7ksnzRL3M6_YKUK_pVw@mail.gmail.com>
Message-ID: <5138BC5B.5080706@stsci.edu>

By default, floating point values are output using 4 decimal points of 
precision.  You can control the amount of precision using the 
"precision" attribute on the field. This is either "F" followed by a 
number of decimal places, or "E" followed by the number of significant 
digits.  For example, when you define your fields, you can do:

# Define some fields
table.fields.extend([
         Field(votable,  name="float",  datatype="double",  precision="E8"))

See also:

http://www.ivoa.net/Documents/VOTable/20040811/REC-VOTable-1.1-20040811.html#ToC26

Mike

On 03/07/2013 06:33 AM, Susana Sanchez Exposito wrote:
> Hello again,
>
> I have followed the instructions given by Tom Aldcroft as answer of my
> previous mail (thanks for that!), and finally I get the xml file with
> the VOTable, but I realized the number are rounded when they are
> written in the xml file.
>
> For example, if I have a table like this:
> (I built this Table following the example in
> https://astropy.readthedocs.org/en/v0.2/io/votable/index.html,
> "Building a new table from scratch"):
>
> In [62]: table
> Out[62]: <astropy.io.votable.tree.Table object at 0x32bcbd0>
>
> In [63]: table.array
> Out[63]:
> masked_rec.array(data = [(17.257360147629999, 18.999976544568401)
>   (13.257360147629999, 78.999976544568398)],
>                   mask = [(False, False) (False, False)],
>             fill_value = (1e+20, 1e+20),
>                  dtype = [('precision', '<f8'), ('precision2', '<f8')])
>
>
> When I build the xml file with the comand votable.to_xml, the file
> contains this data:
>
>   <TABLEDATA>
>       <TR>
>        <TD>17.2574</TD>
>        <TD>19</TD>
>       </TR>
>       <TR>
>        <TD>13.2574</TD>
>        <TD>79</TD>
>       </TR>
>      </TABLEDATA>
>
>
> As you can see, the numbers have been rounded, but I would like to
> preserve the precision of these data. Is this possible?
>
>
> Thanks again for your useful help!
>
> Susana.

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From sse at iaa.es  Fri Mar  8 04:33:00 2013
From: sse at iaa.es (Susana Sanchez Exposito)
Date: Fri, 8 Mar 2013 10:33:00 +0100
Subject: [AstroPy] How can I preserve the precision of the data in the
 votable file?
In-Reply-To: <5138BC5B.5080706@stsci.edu>
References: <CAK=du8+82vyGD1FpTYu6Tc=Rj4YKLfv7ksnzRL3M6_YKUK_pVw@mail.gmail.com>
	<5138BC5B.5080706@stsci.edu>
Message-ID: <CAK=du8JgpsDVYua1PT7K9fj6R791rGzJsADnQtGQk3-Q69-_TQ@mail.gmail.com>

Thanks Mike!!

2013/3/7 Michael Droettboom <mdroe at stsci.edu>:
> By default, floating point values are output using 4 decimal points of
> precision.  You can control the amount of precision using the "precision"
> attribute on the field.  This is either "F" followed by a number of decimal
> places, or "E" followed by the number of significant digits.  For example,
> when you define your fields, you can do:
>
> # Define some fields
> table.fields.extend([
>         Field(votable, name="float", datatype="double", precision="E8"))
>
> See also:
>
> http://www.ivoa.net/Documents/VOTable/20040811/REC-VOTable-1.1-20040811.html#ToC26
>
> Mike
>
>
> On 03/07/2013 06:33 AM, Susana Sanchez Exposito wrote:
>
> Hello again,
>
> I have followed the instructions given by Tom Aldcroft as answer of my
> previous mail (thanks for that!), and finally I get the xml file with
> the VOTable, but I realized the number are rounded when they are
> written in the xml file.
>
> For example, if I have a table like this:
> (I built this Table following the example in
> https://astropy.readthedocs.org/en/v0.2/io/votable/index.html,
> "Building a new table from scratch"):
>
> In [62]: table
> Out[62]: <astropy.io.votable.tree.Table object at 0x32bcbd0>
>
> In [63]: table.array
> Out[63]:
> masked_rec.array(data = [(17.257360147629999, 18.999976544568401)
>  (13.257360147629999, 78.999976544568398)],
>                  mask = [(False, False) (False, False)],
>            fill_value = (1e+20, 1e+20),
>                 dtype = [('precision', '<f8'), ('precision2', '<f8')])
>
>
> When I build the xml file with the comand votable.to_xml, the file
> contains this data:
>
>  <TABLEDATA>
>      <TR>
>       <TD>17.2574</TD>
>       <TD>19</TD>
>      </TR>
>      <TR>
>       <TD>13.2574</TD>
>       <TD>79</TD>
>      </TR>
>     </TABLEDATA>
>
>
> As you can see, the numbers have been rounded, but I would like to
> preserve the precision of these data. Is this possible?
>
>
> Thanks again for your useful help!
>
> Susana.
>
>
>
> _______________________________________________
> AstroPy mailing list
> AstroPy at scipy.org
> http://mail.scipy.org/mailman/listinfo/astropy
>



-- 
Susana S?nchez Exp?sito

Instituto de Astrof?sica de Andaluc?a   IAA (CSIC)
Camino Bajo de Hu?tor, 50. Granada E-18008
Tel:(+34) 958 121 311 / (+34) 958 230 618
Fax:(+34) 958 814 530
e-mail: sse at iaa.es


From mdroe at stsci.edu  Fri Mar  8 09:31:33 2013
From: mdroe at stsci.edu (Michael Droettboom)
Date: Fri, 8 Mar 2013 09:31:33 -0500
Subject: [AstroPy] Fwd: SciPy John Hunter Excellence in Plotting Contest
In-Reply-To: <513928AF.7010201@stsci.edu>
References: <513928AF.7010201@stsci.edu>
Message-ID: <5139F645.3030505@stsci.edu>


Apologies for any accidental cross-posting.

Email not displaying correctly? View it in your browser. 
<http://us1.campaign-archive1.com/?u=e91b4574d5d1709a9dc4f7ab7&id=999d7ba343&e=7c1fb2879c> 


Scientific Computing with Python-Austin, Texas-June 24-29, 2013


  SciPy John Hunter Excellence in Plotting Contest

In memory of John Hunter, we are pleased to announce the first SciPy 
John Hunter Excellence in Plotting Competition. This open competition 
aims to highlight the importance of quality plotting to scientific 
progress and showcase the capabilities of the current generation of 
plotting software. Participants are invited to submit scientific plots 
to be judged by a panel. The winning entries will be announced and 
displayed at the conference.

NumFOCUS is graciously sponsoring cash prizes for the winners in the 
following amounts:

  * 1st prize: $500
  * 2nd prize: $200
  * 3rd prize: $100


    Instructions

  * Entries must be submitted by April 3 via e-mail
    <mailto:plotting-contest at scipy.org>.
  * Plots may be produced with any combination of Python-based tools (it
    is not required that they use matplotlib, for example).
  * Source code for the plot must be provided, along with a rendering of
    the plot in a vector format (PDF, PS, etc.). If the data can not be
    shared for reasons of size or licensing, "fake" data may be
    substituted, along with an image of the plot using real data.
  * Entries will be judged on their clarity, innovation and aesthetics,
    but most importantly for their effectiveness in illuminating real
    scientific work. Entrants are encouraged to submit plots that were
    used during the course of research, rather than merely being
    hypothetical.
  * SciPy reserves the right to display the entry at the conference, use
    in any materials or on its website, providing attribution to the
    original author(s).


    Important dates:

  * April 3rd: Plotting submissions due
  * Monday-Tuesday, June 24 - 25: SciPy 2013 Tutorials, Austin TX
  * Wednesday-Thursday, June 26 - 27: SciPy 2013 Conference, Austin TX *
    Winners will be announced during the conference days
  * Friday-Saturday, June 27 - 28: SciPy 2013 Sprints, Austin TX & remote

We look forward to exciting submissions that push the boundaries of 
plotting, in this, our first attempt at this kind of competition.

The SciPy Plotting Contest Organizer

-Michael Droettboom, Space Telescope Science Institute
You are receiving this email because you subscribed to the mailing list 
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From mdroe at stsci.edu  Thu Mar  7 18:54:23 2013
From: mdroe at stsci.edu (Michael Droettboom)
Date: Thu, 7 Mar 2013 18:54:23 -0500
Subject: [AstroPy] SciPy John Hunter Excellence in Plotting Contest
In-Reply-To: <CAJd6-48F_r3NpnkZW_eA=Z3APu3ULrOXn15aLHcxFayqMqUJng@mail.gmail.com>
References: <CAJd6-48F_r3NpnkZW_eA=Z3APu3ULrOXn15aLHcxFayqMqUJng@mail.gmail.com>
Message-ID: <513928AF.7010201@stsci.edu>

Apologies for any accidental cross-posting.

Email not displaying correctly? View it in your browser. 
<http://us1.campaign-archive1.com/?u=e91b4574d5d1709a9dc4f7ab7&id=999d7ba343&e=7c1fb2879c> 


Scientific Computing with Python-Austin, Texas-June 24-29, 2013


  SciPy John Hunter Excellence in Plotting Contest

In memory of John Hunter, we are pleased to announce the first SciPy 
John Hunter Excellence in Plotting Competition. This open competition 
aims to highlight the importance of quality plotting to scientific 
progress and showcase the capabilities of the current generation of 
plotting software. Participants are invited to submit scientific plots 
to be judged by a panel. The winning entries will be announced and 
displayed at the conference.

NumFOCUS is graciously sponsoring cash prizes for the winners in the 
following amounts:

  * 1st prize: $500
  * 2nd prize: $200
  * 3rd prize: $100


    Instructions

  * Entries must be submitted by April 3 via e-mail
    <mailto:plotting-contest at scipy.org>.
  * Plots may be produced with any combination of Python-based tools (it
    is not required that they use matplotlib, for example).
  * Source code for the plot must be provided, along with a rendering of
    the plot in a vector format (PDF, PS, etc.). If the data can not be
    shared for reasons of size or licensing, "fake" data may be
    substituted, along with an image of the plot using real data.
  * Entries will be judged on their clarity, innovation and aesthetics,
    but most importantly for their effectiveness in illuminating real
    scientific work. Entrants are encouraged to submit plots that were
    used during the course of research, rather than merely being
    hypothetical.
  * SciPy reserves the right to display the entry at the conference, use
    in any materials or on its website, providing attribution to the
    original author(s).


    Important dates:

  * April 3rd: Plotting submissions due
  * Monday-Tuesday, June 24 - 25: SciPy 2013 Tutorials, Austin TX
  * Wednesday-Thursday, June 26 - 27: SciPy 2013 Conference, Austin TX *
    Winners will be announced during the conference days
  * Friday-Saturday, June 27 - 28: SciPy 2013 Sprints, Austin TX & remote

We look forward to exciting submissions that push the boundaries of 
plotting, in this, our first attempt at this kind of competition.

The SciPy Plotting Contest Organizer

-Michael Droettboom, Space Telescope Science Institute
You are receiving this email because you subscribed to the mailing list 
or registered for the SciPy 2010 or SciPy 2011 conference in Austin, TX.

Unsubscribe 
<http://scipy.us1.list-manage.com/unsubscribe?u=e91b4574d5d1709a9dc4f7ab7&id=069dcb6ee4&e=7c1fb2879c&c=999d7ba343> 
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-- 
Michael Droettboom
http://www.droettboom.com/




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From npkuin at gmail.com  Wed Mar 13 13:25:33 2013
From: npkuin at gmail.com (Paul Kuin)
Date: Wed, 13 Mar 2013 17:25:33 +0000
Subject: [AstroPy] fits type of bintable extension
Message-ID: <CANoQ6N2Xyk4BthUsgE+BxdtOgCdMkKZtV9YR_CBxgvq0PR2Oyg@mail.gmail.com>

Hi,

Just looking at the type of one of my bintable extensions and see that it is
astropy.io.fits.hdu.table.BinTableHDU

I was thinking that this makes is a little more difficult to test the
type between the
pyfits and astropy.io.fits packages.

Was this done on purpose or is this a 'feature' ?

Cheers,

   Paul

-- 

* * * * * * * * http://www.mssl.ucl.ac.uk/~npmk/ * * * *
Dr. N.P.M. Kuin      (n.kuin at ucl.ac.uk)
phone +44-(0)1483 (prefix) -204927 (work) -276110 (home)
mobile +44(0)7806985366  skype ID: npkuin
Mullard Space Science Laboratory  ? University College London  ?
Holmbury St Mary ? Dorking ? Surrey RH5 6NT?  U.K.


From arrudy at ucsc.edu  Wed Mar 13 14:07:56 2013
From: arrudy at ucsc.edu (Alexander Rudy)
Date: Wed, 13 Mar 2013 11:07:56 -0700
Subject: [AstroPy] fits type of bintable extension
In-Reply-To: <CANoQ6N2Xyk4BthUsgE+BxdtOgCdMkKZtV9YR_CBxgvq0PR2Oyg@mail.gmail.com>
References: <CANoQ6N2Xyk4BthUsgE+BxdtOgCdMkKZtV9YR_CBxgvq0PR2Oyg@mail.gmail.com>
Message-ID: <CDED7D6F-06AA-468F-9125-B72710811A85@ucsc.edu>

Hi Paul,

What about using the 'isinstance()' built-in method in python?
http://docs.python.org/2/library/functions.html#isinstance
http://docs.python.org/2/library/functions.html#issubclass
That checks the type at runtime, and easily differentiates between them. Try:

>>> import astropy.io.fits.hdu.table
>>> import pyfits.hdu.table
>>> pyFITStable = pyfits.hdu.table.BinTableHDU()
>>> apFITStable = astropy.io.fits.hdu.table.BinTableHDU()
>>> isinstance(pyFITStable,astropy.io.fits.hdu.table.BinTableHDU)
False
>>> isinstance(apFITStable,pyfits.hdu.table.BinTableHDU)
False
>>> isinstance(pyFITStable,pyfits.hdu.table.BinTableHDU)
True

Or, if you want compatibility for both, just use
>>> isinstance(pyFITStable,(pyfits.hdu.table.BinTableHDU,astropy.io.fits.hdu.table.BinTableHDU))
True

I'm not sure what you are looking for here. How are you testing the class differences now? You could register pyfits.hdu.table.BinTableHDU as a subclass of astropy.io.fits.hdu.table.BinTableHDU, but that would only work if HDUs use python's abstract base class construct (which they don't right now). See http://docs.python.org/2/library/abc.html for fun registering subclasses to their superclass.

I hope that helps.

~ Alex

On Mar 13, 2013, at 10:25 , Paul Kuin <npkuin at gmail.com> wrote:

> Hi,
> 
> Just looking at the type of one of my bintable extensions and see that it is
> astropy.io.fits.hdu.table.BinTableHDU
> 
> I was thinking that this makes is a little more difficult to test the
> type between the
> pyfits and astropy.io.fits packages.
> 
> Was this done on purpose or is this a 'feature' ?
> 
> Cheers,
> 
>   Paul
> 
> -- 
> 
> * * * * * * * * http://www.mssl.ucl.ac.uk/~npmk/ * * * *
> Dr. N.P.M. Kuin      (n.kuin at ucl.ac.uk)
> phone +44-(0)1483 (prefix) -204927 (work) -276110 (home)
> mobile +44(0)7806985366  skype ID: npkuin
> Mullard Space Science Laboratory  ? University College London  ?
> Holmbury St Mary ? Dorking ? Surrey RH5 6NT?  U.K.
> _______________________________________________
> AstroPy mailing list
> AstroPy at scipy.org
> http://mail.scipy.org/mailman/listinfo/astropy



From thomas.robitaille at gmail.com  Wed Mar 13 14:11:26 2013
From: thomas.robitaille at gmail.com (Thomas Robitaille)
Date: Wed, 13 Mar 2013 19:11:26 +0100
Subject: [AstroPy] fits type of bintable extension
In-Reply-To: <CANoQ6N2Xyk4BthUsgE+BxdtOgCdMkKZtV9YR_CBxgvq0PR2Oyg@mail.gmail.com>
References: <CANoQ6N2Xyk4BthUsgE+BxdtOgCdMkKZtV9YR_CBxgvq0PR2Oyg@mail.gmail.com>
Message-ID: <CAGMHX_2ewx804y72kQLrHem9vYWv8dFMWRcwB6JCaNL4TXNknQ@mail.gmail.com>

Hi Paul,

It isn't a feature or bug, it's more just to do with the fact that the
pyfits package is now in astropy.io.fits, so the path to the classes
has changed. As Alex pointed out, you can use isinstance(), but note
that you can use pyfits.BinTableHDU and astropy.io.fits.BinTableHDU
for conciseness (you don't need the .hdu.table. part) since the
classes are imported into the top level of pyfits and astropy.io.fits.

FYI, If you want to use Astropy instead of PyFITS with minimal changes
to scripts, you can do:

from astropy.io import fits as pyfits

and the rest of the script will not need to be modified.

Cheers,
Tom


On 13 March 2013 18:25, Paul Kuin <npkuin at gmail.com> wrote:
> Hi,
>
> Just looking at the type of one of my bintable extensions and see that it is
> astropy.io.fits.hdu.table.BinTableHDU
>
> I was thinking that this makes is a little more difficult to test the
> type between the
> pyfits and astropy.io.fits packages.
>
> Was this done on purpose or is this a 'feature' ?
>
> Cheers,
>
>    Paul
>
> --
>
> * * * * * * * * http://www.mssl.ucl.ac.uk/~npmk/ * * * *
> Dr. N.P.M. Kuin      (n.kuin at ucl.ac.uk)
> phone +44-(0)1483 (prefix) -204927 (work) -276110 (home)
> mobile +44(0)7806985366  skype ID: npkuin
> Mullard Space Science Laboratory  ? University College London  ?
> Holmbury St Mary ? Dorking ? Surrey RH5 6NT?  U.K.
> _______________________________________________
> AstroPy mailing list
> AstroPy at scipy.org
> http://mail.scipy.org/mailman/listinfo/astropy


From abhijithrajan at asu.edu  Wed Mar 13 16:53:33 2013
From: abhijithrajan at asu.edu (Abhijith Rajan)
Date: Wed, 13 Mar 2013 13:53:33 -0700
Subject: [AstroPy] great circle?
Message-ID: <CAHfbfxHK-vHKBFqKjLk=R_t6LdnVBo=QYBgmqx7d1RE+He-NDw@mail.gmail.com>

Hi,

Just wondering if there is a convenient python module to compute the great
circle distance similar to gcirc.pro in IDL?

Thanks
Abhi

p.s: I realize its only ~10 lines of code and I plan to implement it for my
immediate needs.
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From aldcroft at head.cfa.harvard.edu  Wed Mar 13 17:11:40 2013
From: aldcroft at head.cfa.harvard.edu (Tom Aldcroft)
Date: Wed, 13 Mar 2013 17:11:40 -0400
Subject: [AstroPy] great circle?
In-Reply-To: <CAHfbfxHK-vHKBFqKjLk=R_t6LdnVBo=QYBgmqx7d1RE+He-NDw@mail.gmail.com>
References: <CAHfbfxHK-vHKBFqKjLk=R_t6LdnVBo=QYBgmqx7d1RE+He-NDw@mail.gmail.com>
Message-ID: <CAGsQ-NvXAEvsWFhcyL9c9XX17qHx9LkGLBcT6FRUe0u6b7kMRQ@mail.gmail.com>

On Wed, Mar 13, 2013 at 4:53 PM, Abhijith Rajan <abhijithrajan at asu.edu> wrote:
> Hi,
>
> Just wondering if there is a convenient python module to compute the great
> circle distance similar to gcirc.pro in IDL?

Yes, use the separation() method in astropy.coordinates:

  http://docs.astropy.org/en/v0.2/coordinates/separations.html

Cheers,
Tom


>
> Thanks
> Abhi
>
> p.s: I realize its only ~10 lines of code and I plan to implement it for my
> immediate needs.
>
> _______________________________________________
> AstroPy mailing list
> AstroPy at scipy.org
> http://mail.scipy.org/mailman/listinfo/astropy
>


From abhijithrajan at asu.edu  Wed Mar 13 17:20:32 2013
From: abhijithrajan at asu.edu (Abhijith Rajan)
Date: Wed, 13 Mar 2013 14:20:32 -0700
Subject: [AstroPy] great circle?
In-Reply-To: <CAGsQ-NvXAEvsWFhcyL9c9XX17qHx9LkGLBcT6FRUe0u6b7kMRQ@mail.gmail.com>
References: <CAHfbfxHK-vHKBFqKjLk=R_t6LdnVBo=QYBgmqx7d1RE+He-NDw@mail.gmail.com>
	<CAGsQ-NvXAEvsWFhcyL9c9XX17qHx9LkGLBcT6FRUe0u6b7kMRQ@mail.gmail.com>
Message-ID: <CAHfbfxGxnU68770435prvq7T+pDqK_jQVijevnV36DibQBSVJw@mail.gmail.com>

Excellent. Thanks :).

Abhi

On Wed, Mar 13, 2013 at 2:11 PM, Tom Aldcroft <aldcroft at head.cfa.harvard.edu
> wrote:

> On Wed, Mar 13, 2013 at 4:53 PM, Abhijith Rajan <abhijithrajan at asu.edu>
> wrote:
> > Hi,
> >
> > Just wondering if there is a convenient python module to compute the
> great
> > circle distance similar to gcirc.pro in IDL?
>
> Yes, use the separation() method in astropy.coordinates:
>
>   http://docs.astropy.org/en/v0.2/coordinates/separations.html
>
> Cheers,
> Tom
>
>
> >
> > Thanks
> > Abhi
> >
> > p.s: I realize its only ~10 lines of code and I plan to implement it for
> my
> > immediate needs.
> >
> > _______________________________________________
> > AstroPy mailing list
> > AstroPy at scipy.org
> > http://mail.scipy.org/mailman/listinfo/astropy
> >
>
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From thomas.robitaille at gmail.com  Mon Mar 18 12:59:54 2013
From: thomas.robitaille at gmail.com (Thomas Robitaille)
Date: Mon, 18 Mar 2013 17:59:54 +0100
Subject: [AstroPy] montage-wrapper v0.9.5 release
Message-ID: <CAGMHX_1N7=MaeB9y-8RcrQUFUAPmyOU=Etf6OD0uuW=ajG-53g@mail.gmail.com>

I am pleased to announce the release of montage-wrapper v0.9.5
(formerly python-montage). Montage-wrapper is a package that provides
a way to run the Montage Astronomical Image Mosaic Engine from Python,
including both functions to access individual Montage commands, and
high-level functions to facilitate mosaicking and reprojecting.

Montage-wrapper is now an Astropy-affiliated package, which means that
it follows the Astropy guidelines for packages, and requires Astropy
as a dependency. In addition, this release includes a number of bug
fixes and stability/performance improvements. The homepage is now
located at:

 http://www.astropy.org/montage-wrapper/

and the documentation can be found here:

 http://montage-wrapper.readthedocs.org/

Please note that due to the change in the name of the package, the
module should now be imported with:

 import montage_wrapper

In order to get old scripts to work, or generally for convenience, you
can import the module with:

 import montage_wrapper as montage

(the change in package name from 'montage' to 'montage_wrapper' is to
avoid conflict with another package named 'montage')

Please report any issues either via GitHub at:

 https://github.com/astropy/montage-wrapper/issues

or directly to me by email.

Cheers, Tom


From jslavin at cfa.harvard.edu  Thu Mar 21 14:20:37 2013
From: jslavin at cfa.harvard.edu (Jonathan Slavin)
Date: Thu, 21 Mar 2013 14:20:37 -0400
Subject: [AstroPy] why the warning about Converting Quantity?
Message-ID: <1363890037.4653.6.camel@shevek>

Hi,

I have just used the constants module in astropy for the first time and
got 6 warnings from my code as a result:

import astropy.constants as const
AU = const.au.to('km')

leads to 
WARNING: Converting Quantity object in units 'km' to a Numpy array
[astropy.units.quantity]
WARNING: Converting Quantity object in units 'km' to a Numpy array
[astropy.units.quantity]
WARNING: Converting Quantity object in units 'km' to a Numpy array
[astropy.units.quantity]
WARNING: Converting Quantity object in units 'km' to a Numpy array
[astropy.units.quantity]
WARNING: Converting Quantity object in units 'km' to a Numpy array
[astropy.units.quantity]
WARNING: Converting Quantity object in units 'km' to a Numpy array
[astropy.units.quantity]

It seems that I get the warning every place I use the value of AU.  Do I
have to turn off warnings  to prevent this?  Is there some other way to
deal with this?

Jon
-- 
______________________________________________________________
Jonathan D. Slavin              Harvard-Smithsonian CfA
jslavin at cfa.harvard.edu         60 Garden Street, MS 83
phone: (617) 496-7981           Cambridge, MA 02138-1516
 cell: (781) 363-0035           USA
______________________________________________________________



From adrianmpw at gmail.com  Thu Mar 21 15:05:14 2013
From: adrianmpw at gmail.com (Adrian Price-Whelan)
Date: Thu, 21 Mar 2013 15:05:14 -0400
Subject: [AstroPy] why the warning about Converting Quantity?
In-Reply-To: <1363890037.4653.6.camel@shevek>
References: <1363890037.4653.6.camel@shevek>
Message-ID: <1F835E06-111A-4D79-B703-D08CE549D665@gmail.com>

Hey Jonathan --

Are you sure that's the point in the code that's producing the warning? What operations are you doing with the AU object? When you use the .to() method, it still returns a Quantity object -- *not* the value of the original object in those units. If you then stick AU into any numpy function, it will work but will just extract the value from the object (hence the warning). 

See, for example:

>>> import astropy.units as u
>>> np.sqrt(15*u.km)
WARNING: Converting Quantity object in units 'km' to a Numpy array [astropy.units.quantity]
3.872983346207417

To turn this off, you'll want to set:
>>> u.quantity.WARN_IMPLICIT_NUMERIC_CONVERSION.set(False)
>>> np.sqrt(15*u.km)
3.872983346207417

Note that this is documented in the astropy.units.quantity section of the astropy documentation:
http://docs.astropy.org/en/latest/units/quantity.html#converting-to-python-or-numpy-types

Thanks,
Adrian

On Mar 21, 2013, at 2:20 PM, Jonathan Slavin wrote:

> Hi,
> 
> I have just used the constants module in astropy for the first time and
> got 6 warnings from my code as a result:
> 
> import astropy.constants as const
> AU = const.au.to('km')
> 
> leads to 
> WARNING: Converting Quantity object in units 'km' to a Numpy array
> [astropy.units.quantity]
> WARNING: Converting Quantity object in units 'km' to a Numpy array
> [astropy.units.quantity]
> WARNING: Converting Quantity object in units 'km' to a Numpy array
> [astropy.units.quantity]
> WARNING: Converting Quantity object in units 'km' to a Numpy array
> [astropy.units.quantity]
> WARNING: Converting Quantity object in units 'km' to a Numpy array
> [astropy.units.quantity]
> WARNING: Converting Quantity object in units 'km' to a Numpy array
> [astropy.units.quantity]
> 
> It seems that I get the warning every place I use the value of AU.  Do I
> have to turn off warnings  to prevent this?  Is there some other way to
> deal with this?
> 
> Jon
> -- 
> ______________________________________________________________
> Jonathan D. Slavin              Harvard-Smithsonian CfA
> jslavin at cfa.harvard.edu         60 Garden Street, MS 83
> phone: (617) 496-7981           Cambridge, MA 02138-1516
> cell: (781) 363-0035           USA
> ______________________________________________________________
> 
> _______________________________________________
> AstroPy mailing list
> AstroPy at scipy.org
> http://mail.scipy.org/mailman/listinfo/astropy

--
Adrian Price-Whelan
Department of Astronomy
Columbia University





From wkerzendorf at gmail.com  Thu Mar 21 15:15:26 2013
From: wkerzendorf at gmail.com (Wolfgang Kerzendorf)
Date: Thu, 21 Mar 2013 15:15:26 -0400
Subject: [AstroPy] why the warning about Converting Quantity?
In-Reply-To: <1F835E06-111A-4D79-B703-D08CE549D665@gmail.com>
References: <1363890037.4653.6.camel@shevek>
	<1F835E06-111A-4D79-B703-D08CE549D665@gmail.com>
Message-ID: <4C0F654A-D6CB-4093-BAC9-8D3F28A5C485@gmail.com>

Hi Jonathan,

I think, one should not turn this warning off. It warns you that the quantity you get after the operations does not necessarily have the same units as before - and rightly so. 
When doing things like np.sqrt(15* u.km), they can be replaced with np.sqrt((15 * u.km).value) which specifically tells it to convert to a float (and puts the onus on you to think about the units). 

Cheers
   Wolfgang

Hope that helps
On 2013-03-21, at 3:05 PM, Adrian Price-Whelan <adrianmpw at gmail.com> wrote:

> Hey Jonathan --
> 
> Are you sure that's the point in the code that's producing the warning? What operations are you doing with the AU object? When you use the .to() method, it still returns a Quantity object -- *not* the value of the original object in those units. If you then stick AU into any numpy function, it will work but will just extract the value from the object (hence the warning). 
> 
> See, for example:
> 
>>>> import astropy.units as u
>>>> np.sqrt(15*u.km)
> WARNING: Converting Quantity object in units 'km' to a Numpy array [astropy.units.quantity]
> 3.872983346207417
> 
> To turn this off, you'll want to set:
>>>> u.quantity.WARN_IMPLICIT_NUMERIC_CONVERSION.set(False)
>>>> np.sqrt(15*u.km)
> 3.872983346207417
> 
> Note that this is documented in the astropy.units.quantity section of the astropy documentation:
> http://docs.astropy.org/en/latest/units/quantity.html#converting-to-python-or-numpy-types
> 
> Thanks,
> Adrian
> 
> On Mar 21, 2013, at 2:20 PM, Jonathan Slavin wrote:
> 
>> Hi,
>> 
>> I have just used the constants module in astropy for the first time and
>> got 6 warnings from my code as a result:
>> 
>> import astropy.constants as const
>> AU = const.au.to('km')
>> 
>> leads to 
>> WARNING: Converting Quantity object in units 'km' to a Numpy array
>> [astropy.units.quantity]
>> WARNING: Converting Quantity object in units 'km' to a Numpy array
>> [astropy.units.quantity]
>> WARNING: Converting Quantity object in units 'km' to a Numpy array
>> [astropy.units.quantity]
>> WARNING: Converting Quantity object in units 'km' to a Numpy array
>> [astropy.units.quantity]
>> WARNING: Converting Quantity object in units 'km' to a Numpy array
>> [astropy.units.quantity]
>> WARNING: Converting Quantity object in units 'km' to a Numpy array
>> [astropy.units.quantity]
>> 
>> It seems that I get the warning every place I use the value of AU.  Do I
>> have to turn off warnings  to prevent this?  Is there some other way to
>> deal with this?
>> 
>> Jon
>> -- 
>> ______________________________________________________________
>> Jonathan D. Slavin              Harvard-Smithsonian CfA
>> jslavin at cfa.harvard.edu         60 Garden Street, MS 83
>> phone: (617) 496-7981           Cambridge, MA 02138-1516
>> cell: (781) 363-0035           USA
>> ______________________________________________________________
>> 
>> _______________________________________________
>> AstroPy mailing list
>> AstroPy at scipy.org
>> http://mail.scipy.org/mailman/listinfo/astropy
> 
> --
> Adrian Price-Whelan
> Department of Astronomy
> Columbia University
> 
> 
> 
> _______________________________________________
> AstroPy mailing list
> AstroPy at scipy.org
> http://mail.scipy.org/mailman/listinfo/astropy



From jslavin at cfa.harvard.edu  Thu Mar 21 15:22:50 2013
From: jslavin at cfa.harvard.edu (Jonathan Slavin)
Date: Thu, 21 Mar 2013 15:22:50 -0400
Subject: [AstroPy] why the warning about Converting Quantity?
In-Reply-To: <1F835E06-111A-4D79-B703-D08CE549D665@gmail.com>
References: <1363890037.4653.6.camel@shevek>
	<1F835E06-111A-4D79-B703-D08CE549D665@gmail.com>
Message-ID: <1363893770.8743.12.camel@shevek>

Hi Adrian,

Yes, as I mentioned farther down in my post, the warnings are generated
when I use it in an expression -- with numpy arrays.  It'd be nice to
have a less cumbersome way of suppressing those warnings (yes it's just
one line, but not so easy to remember).  In fact, I would expect to use
the constants mostly in expressions with numpy arrays, variables, etc.
that don't have units, so my preference would be that by default those
warnings are turned off -- at least for the constants.  The constants
are useful for their values alone, though clearly the value of the units
module is to associate units with values.  Maybe a simple method like
value.asfloat() could be added that would allow conversion from a units
object to a numpy float.

Jon

On Thu, 2013-03-21 at 15:05 -0400, Adrian Price-Whelan wrote:
> Hey Jonathan --
> 
> Are you sure that's the point in the code that's producing the
> warning? What operations are you doing with the AU object? When you
> use the .to() method, it still returns a Quantity object -- *not* the
> value of the original object in those units. If you then stick AU into
> any numpy function, it will work but will just extract the value from
> the object (hence the warning). 
> 
> See, for example:
> 
> >>> import astropy.units as u
> >>> np.sqrt(15*u.km)
> WARNING: Converting Quantity object in units 'km' to a Numpy array
> [astropy.units.quantity]
> 3.872983346207417
> 
> To turn this off, you'll want to set:
> >>> u.quantity.WARN_IMPLICIT_NUMERIC_CONVERSION.set(False)
> >>> np.sqrt(15*u.km)
> 3.872983346207417
> 
> Note that this is documented in the astropy.units.quantity section of
> the astropy documentation:
> http://docs.astropy.org/en/latest/units/quantity.html#converting-to-python-or-numpy-types
> 
> Thanks,
> Adrian
> 
> On Mar 21, 2013, at 2:20 PM, Jonathan Slavin wrote:
> 
> > Hi,
> > 
> > I have just used the constants module in astropy for the first time and
> > got 6 warnings from my code as a result:
> > 
> > import astropy.constants as const
> > AU = const.au.to('km')
> > 
> > leads to 
> > WARNING: Converting Quantity object in units 'km' to a Numpy array
> > [astropy.units.quantity]
> > WARNING: Converting Quantity object in units 'km' to a Numpy array
> > [astropy.units.quantity]
> > WARNING: Converting Quantity object in units 'km' to a Numpy array
> > [astropy.units.quantity]
> > WARNING: Converting Quantity object in units 'km' to a Numpy array
> > [astropy.units.quantity]
> > WARNING: Converting Quantity object in units 'km' to a Numpy array
> > [astropy.units.quantity]
> > WARNING: Converting Quantity object in units 'km' to a Numpy array
> > [astropy.units.quantity]
> > 
> > It seems that I get the warning every place I use the value of AU.  Do I
> > have to turn off warnings  to prevent this?  Is there some other way to
> > deal with this?
> > 
> > Jon
> > -- 
> > ______________________________________________________________
> > Jonathan D. Slavin              Harvard-Smithsonian CfA
> > jslavin at cfa.harvard.edu         60 Garden Street, MS 83
> > phone: (617) 496-7981           Cambridge, MA 02138-1516
> > cell: (781) 363-0035           USA
> > ______________________________________________________________
> > 
> > _______________________________________________
> > AstroPy mailing list
> > AstroPy at scipy.org
> > http://mail.scipy.org/mailman/listinfo/astropy
> 
> --
> Adrian Price-Whelan
> Department of Astronomy
> Columbia University
> 
> 
> 

-- 
______________________________________________________________
Jonathan D. Slavin              Harvard-Smithsonian CfA
jslavin at cfa.harvard.edu         60 Garden Street, MS 83
phone: (617) 496-7981           Cambridge, MA 02138-1516
 cell: (781) 363-0035           USA
______________________________________________________________



From erik.tollerud at gmail.com  Fri Mar 22 10:57:35 2013
From: erik.tollerud at gmail.com (Erik Tollerud)
Date: Fri, 22 Mar 2013 10:57:35 -0400
Subject: [AstroPy] why the warning about Converting Quantity?
In-Reply-To: <1363893770.8743.12.camel@shevek>
References: <1363890037.4653.6.camel@shevek>
	<1F835E06-111A-4D79-B703-D08CE549D665@gmail.com>
	<1363893770.8743.12.camel@shevek>
Message-ID: <CAARXUwWmhzPXSr8ieRw+7hwkuQaT8k4Yfm3OW=fLVAs7SGbSDw@mail.gmail.com>

Hello Jonathan et al.,

I think some confusion here stems from the fact that ``AU`` is a bit
of a special constant - in most cases, you're probably better off
using the AU *unit*, rather than the constant.  That is, if you were
doing something like

arrinau = arr * constants.au

That gives exactly the warning you mentioned, whereas

arrinau = arr * units.au

won't give out a warning, because it creates a `Quantity` object with
the units `AU`, rather than a regular array without any units.


Does that make sense, or am I still misunderstanding how you're using
this? If the latter, can you give an actual example of the line that
actually produces this warning? That'll make it easier to understand
exactly what you're suggesting.




On Thu, Mar 21, 2013 at 3:22 PM, Jonathan Slavin
<jslavin at cfa.harvard.edu> wrote:
> Hi Adrian,
>
> Yes, as I mentioned farther down in my post, the warnings are generated
> when I use it in an expression -- with numpy arrays.  It'd be nice to
> have a less cumbersome way of suppressing those warnings (yes it's just
> one line, but not so easy to remember).  In fact, I would expect to use
> the constants mostly in expressions with numpy arrays, variables, etc.
> that don't have units, so my preference would be that by default those
> warnings are turned off -- at least for the constants.  The constants
> are useful for their values alone, though clearly the value of the units
> module is to associate units with values.  Maybe a simple method like
> value.asfloat() could be added that would allow conversion from a units
> object to a numpy float.
>
> Jon
>
> On Thu, 2013-03-21 at 15:05 -0400, Adrian Price-Whelan wrote:
>> Hey Jonathan --
>>
>> Are you sure that's the point in the code that's producing the
>> warning? What operations are you doing with the AU object? When you
>> use the .to() method, it still returns a Quantity object -- *not* the
>> value of the original object in those units. If you then stick AU into
>> any numpy function, it will work but will just extract the value from
>> the object (hence the warning).
>>
>> See, for example:
>>
>> >>> import astropy.units as u
>> >>> np.sqrt(15*u.km)
>> WARNING: Converting Quantity object in units 'km' to a Numpy array
>> [astropy.units.quantity]
>> 3.872983346207417
>>
>> To turn this off, you'll want to set:
>> >>> u.quantity.WARN_IMPLICIT_NUMERIC_CONVERSION.set(False)
>> >>> np.sqrt(15*u.km)
>> 3.872983346207417
>>
>> Note that this is documented in the astropy.units.quantity section of
>> the astropy documentation:
>> http://docs.astropy.org/en/latest/units/quantity.html#converting-to-python-or-numpy-types
>>
>> Thanks,
>> Adrian
>>
>> On Mar 21, 2013, at 2:20 PM, Jonathan Slavin wrote:
>>
>> > Hi,
>> >
>> > I have just used the constants module in astropy for the first time and
>> > got 6 warnings from my code as a result:
>> >
>> > import astropy.constants as const
>> > AU = const.au.to('km')
>> >
>> > leads to
>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>> > [astropy.units.quantity]
>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>> > [astropy.units.quantity]
>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>> > [astropy.units.quantity]
>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>> > [astropy.units.quantity]
>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>> > [astropy.units.quantity]
>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>> > [astropy.units.quantity]
>> >
>> > It seems that I get the warning every place I use the value of AU.  Do I
>> > have to turn off warnings  to prevent this?  Is there some other way to
>> > deal with this?
>> >
>> > Jon
>> > --
>> > ______________________________________________________________
>> > Jonathan D. Slavin              Harvard-Smithsonian CfA
>> > jslavin at cfa.harvard.edu         60 Garden Street, MS 83
>> > phone: (617) 496-7981           Cambridge, MA 02138-1516
>> > cell: (781) 363-0035           USA
>> > ______________________________________________________________
>> >
>> > _______________________________________________
>> > AstroPy mailing list
>> > AstroPy at scipy.org
>> > http://mail.scipy.org/mailman/listinfo/astropy
>>
>> --
>> Adrian Price-Whelan
>> Department of Astronomy
>> Columbia University
>>
>>
>>
>
> --
> ______________________________________________________________
> Jonathan D. Slavin              Harvard-Smithsonian CfA
> jslavin at cfa.harvard.edu         60 Garden Street, MS 83
> phone: (617) 496-7981           Cambridge, MA 02138-1516
>  cell: (781) 363-0035           USA
> ______________________________________________________________
>
> _______________________________________________
> AstroPy mailing list
> AstroPy at scipy.org
> http://mail.scipy.org/mailman/listinfo/astropy



--
Erik

On Thu, Mar 21, 2013 at 3:22 PM, Jonathan Slavin
<jslavin at cfa.harvard.edu> wrote:
> Hi Adrian,
>
> Yes, as I mentioned farther down in my post, the warnings are generated
> when I use it in an expression -- with numpy arrays.  It'd be nice to
> have a less cumbersome way of suppressing those warnings (yes it's just
> one line, but not so easy to remember).  In fact, I would expect to use
> the constants mostly in expressions with numpy arrays, variables, etc.
> that don't have units, so my preference would be that by default those
> warnings are turned off -- at least for the constants.  The constants
> are useful for their values alone, though clearly the value of the units
> module is to associate units with values.  Maybe a simple method like
> value.asfloat() could be added that would allow conversion from a units
> object to a numpy float.
>
> Jon
>
> On Thu, 2013-03-21 at 15:05 -0400, Adrian Price-Whelan wrote:
>> Hey Jonathan --
>>
>> Are you sure that's the point in the code that's producing the
>> warning? What operations are you doing with the AU object? When you
>> use the .to() method, it still returns a Quantity object -- *not* the
>> value of the original object in those units. If you then stick AU into
>> any numpy function, it will work but will just extract the value from
>> the object (hence the warning).
>>
>> See, for example:
>>
>> >>> import astropy.units as u
>> >>> np.sqrt(15*u.km)
>> WARNING: Converting Quantity object in units 'km' to a Numpy array
>> [astropy.units.quantity]
>> 3.872983346207417
>>
>> To turn this off, you'll want to set:
>> >>> u.quantity.WARN_IMPLICIT_NUMERIC_CONVERSION.set(False)
>> >>> np.sqrt(15*u.km)
>> 3.872983346207417
>>
>> Note that this is documented in the astropy.units.quantity section of
>> the astropy documentation:
>> http://docs.astropy.org/en/latest/units/quantity.html#converting-to-python-or-numpy-types
>>
>> Thanks,
>> Adrian
>>
>> On Mar 21, 2013, at 2:20 PM, Jonathan Slavin wrote:
>>
>> > Hi,
>> >
>> > I have just used the constants module in astropy for the first time and
>> > got 6 warnings from my code as a result:
>> >
>> > import astropy.constants as const
>> > AU = const.au.to('km')
>> >
>> > leads to
>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>> > [astropy.units.quantity]
>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>> > [astropy.units.quantity]
>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>> > [astropy.units.quantity]
>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>> > [astropy.units.quantity]
>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>> > [astropy.units.quantity]
>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>> > [astropy.units.quantity]
>> >
>> > It seems that I get the warning every place I use the value of AU.  Do I
>> > have to turn off warnings  to prevent this?  Is there some other way to
>> > deal with this?
>> >
>> > Jon
>> > --
>> > ______________________________________________________________
>> > Jonathan D. Slavin              Harvard-Smithsonian CfA
>> > jslavin at cfa.harvard.edu         60 Garden Street, MS 83
>> > phone: (617) 496-7981           Cambridge, MA 02138-1516
>> > cell: (781) 363-0035           USA
>> > ______________________________________________________________
>> >
>> > _______________________________________________
>> > AstroPy mailing list
>> > AstroPy at scipy.org
>> > http://mail.scipy.org/mailman/listinfo/astropy
>>
>> --
>> Adrian Price-Whelan
>> Department of Astronomy
>> Columbia University
>>
>>
>>
>
> --
> ______________________________________________________________
> Jonathan D. Slavin              Harvard-Smithsonian CfA
> jslavin at cfa.harvard.edu         60 Garden Street, MS 83
> phone: (617) 496-7981           Cambridge, MA 02138-1516
>  cell: (781) 363-0035           USA
> ______________________________________________________________
>
> _______________________________________________
> AstroPy mailing list
> AstroPy at scipy.org
> http://mail.scipy.org/mailman/listinfo/astropy



--
Erik Tollerud


From thomas.robitaille at gmail.com  Fri Mar 22 11:18:53 2013
From: thomas.robitaille at gmail.com (Thomas Robitaille)
Date: Fri, 22 Mar 2013 16:18:53 +0100
Subject: [AstroPy] why the warning about Converting Quantity?
In-Reply-To: <CAARXUwWmhzPXSr8ieRw+7hwkuQaT8k4Yfm3OW=fLVAs7SGbSDw@mail.gmail.com>
References: <1363890037.4653.6.camel@shevek>
	<1F835E06-111A-4D79-B703-D08CE549D665@gmail.com>
	<1363893770.8743.12.camel@shevek>
	<CAARXUwWmhzPXSr8ieRw+7hwkuQaT8k4Yfm3OW=fLVAs7SGbSDw@mail.gmail.com>
Message-ID: <CAGMHX_3vtgXiuLRJPh9RDhzH5F1sCj3+bLu163ZrT8kmQ4+eSw@mail.gmail.com>

I think that

In [4]: np.array([1,2,3]) * constants.au
WARNING: Converting Quantity object in units 'm' to a Numpy array
[astropy.units.quantity]
Out[4]: array([  1.49597871e+11,   2.99195741e+11,   4.48793612e+11])

is actually a bug, as this should return a Quantity (like it does for
scalars). I'll submit a PR shortly.

Cheers,
Tom

On 22 March 2013 15:57, Erik Tollerud <erik.tollerud at gmail.com> wrote:
> Hello Jonathan et al.,
>
> I think some confusion here stems from the fact that ``AU`` is a bit
> of a special constant - in most cases, you're probably better off
> using the AU *unit*, rather than the constant.  That is, if you were
> doing something like
>
> arrinau = arr * constants.au
>
> That gives exactly the warning you mentioned, whereas
>
> arrinau = arr * units.au
>
> won't give out a warning, because it creates a `Quantity` object with
> the units `AU`, rather than a regular array without any units.
>
>
> Does that make sense, or am I still misunderstanding how you're using
> this? If the latter, can you give an actual example of the line that
> actually produces this warning? That'll make it easier to understand
> exactly what you're suggesting.
>
>
>
>
> On Thu, Mar 21, 2013 at 3:22 PM, Jonathan Slavin
> <jslavin at cfa.harvard.edu> wrote:
>> Hi Adrian,
>>
>> Yes, as I mentioned farther down in my post, the warnings are generated
>> when I use it in an expression -- with numpy arrays.  It'd be nice to
>> have a less cumbersome way of suppressing those warnings (yes it's just
>> one line, but not so easy to remember).  In fact, I would expect to use
>> the constants mostly in expressions with numpy arrays, variables, etc.
>> that don't have units, so my preference would be that by default those
>> warnings are turned off -- at least for the constants.  The constants
>> are useful for their values alone, though clearly the value of the units
>> module is to associate units with values.  Maybe a simple method like
>> value.asfloat() could be added that would allow conversion from a units
>> object to a numpy float.
>>
>> Jon
>>
>> On Thu, 2013-03-21 at 15:05 -0400, Adrian Price-Whelan wrote:
>>> Hey Jonathan --
>>>
>>> Are you sure that's the point in the code that's producing the
>>> warning? What operations are you doing with the AU object? When you
>>> use the .to() method, it still returns a Quantity object -- *not* the
>>> value of the original object in those units. If you then stick AU into
>>> any numpy function, it will work but will just extract the value from
>>> the object (hence the warning).
>>>
>>> See, for example:
>>>
>>> >>> import astropy.units as u
>>> >>> np.sqrt(15*u.km)
>>> WARNING: Converting Quantity object in units 'km' to a Numpy array
>>> [astropy.units.quantity]
>>> 3.872983346207417
>>>
>>> To turn this off, you'll want to set:
>>> >>> u.quantity.WARN_IMPLICIT_NUMERIC_CONVERSION.set(False)
>>> >>> np.sqrt(15*u.km)
>>> 3.872983346207417
>>>
>>> Note that this is documented in the astropy.units.quantity section of
>>> the astropy documentation:
>>> http://docs.astropy.org/en/latest/units/quantity.html#converting-to-python-or-numpy-types
>>>
>>> Thanks,
>>> Adrian
>>>
>>> On Mar 21, 2013, at 2:20 PM, Jonathan Slavin wrote:
>>>
>>> > Hi,
>>> >
>>> > I have just used the constants module in astropy for the first time and
>>> > got 6 warnings from my code as a result:
>>> >
>>> > import astropy.constants as const
>>> > AU = const.au.to('km')
>>> >
>>> > leads to
>>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>>> > [astropy.units.quantity]
>>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>>> > [astropy.units.quantity]
>>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>>> > [astropy.units.quantity]
>>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>>> > [astropy.units.quantity]
>>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>>> > [astropy.units.quantity]
>>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>>> > [astropy.units.quantity]
>>> >
>>> > It seems that I get the warning every place I use the value of AU.  Do I
>>> > have to turn off warnings  to prevent this?  Is there some other way to
>>> > deal with this?
>>> >
>>> > Jon
>>> > --
>>> > ______________________________________________________________
>>> > Jonathan D. Slavin              Harvard-Smithsonian CfA
>>> > jslavin at cfa.harvard.edu         60 Garden Street, MS 83
>>> > phone: (617) 496-7981           Cambridge, MA 02138-1516
>>> > cell: (781) 363-0035           USA
>>> > ______________________________________________________________
>>> >
>>> > _______________________________________________
>>> > AstroPy mailing list
>>> > AstroPy at scipy.org
>>> > http://mail.scipy.org/mailman/listinfo/astropy
>>>
>>> --
>>> Adrian Price-Whelan
>>> Department of Astronomy
>>> Columbia University
>>>
>>>
>>>
>>
>> --
>> ______________________________________________________________
>> Jonathan D. Slavin              Harvard-Smithsonian CfA
>> jslavin at cfa.harvard.edu         60 Garden Street, MS 83
>> phone: (617) 496-7981           Cambridge, MA 02138-1516
>>  cell: (781) 363-0035           USA
>> ______________________________________________________________
>>
>> _______________________________________________
>> AstroPy mailing list
>> AstroPy at scipy.org
>> http://mail.scipy.org/mailman/listinfo/astropy
>
>
>
> --
> Erik
>
> On Thu, Mar 21, 2013 at 3:22 PM, Jonathan Slavin
> <jslavin at cfa.harvard.edu> wrote:
>> Hi Adrian,
>>
>> Yes, as I mentioned farther down in my post, the warnings are generated
>> when I use it in an expression -- with numpy arrays.  It'd be nice to
>> have a less cumbersome way of suppressing those warnings (yes it's just
>> one line, but not so easy to remember).  In fact, I would expect to use
>> the constants mostly in expressions with numpy arrays, variables, etc.
>> that don't have units, so my preference would be that by default those
>> warnings are turned off -- at least for the constants.  The constants
>> are useful for their values alone, though clearly the value of the units
>> module is to associate units with values.  Maybe a simple method like
>> value.asfloat() could be added that would allow conversion from a units
>> object to a numpy float.
>>
>> Jon
>>
>> On Thu, 2013-03-21 at 15:05 -0400, Adrian Price-Whelan wrote:
>>> Hey Jonathan --
>>>
>>> Are you sure that's the point in the code that's producing the
>>> warning? What operations are you doing with the AU object? When you
>>> use the .to() method, it still returns a Quantity object -- *not* the
>>> value of the original object in those units. If you then stick AU into
>>> any numpy function, it will work but will just extract the value from
>>> the object (hence the warning).
>>>
>>> See, for example:
>>>
>>> >>> import astropy.units as u
>>> >>> np.sqrt(15*u.km)
>>> WARNING: Converting Quantity object in units 'km' to a Numpy array
>>> [astropy.units.quantity]
>>> 3.872983346207417
>>>
>>> To turn this off, you'll want to set:
>>> >>> u.quantity.WARN_IMPLICIT_NUMERIC_CONVERSION.set(False)
>>> >>> np.sqrt(15*u.km)
>>> 3.872983346207417
>>>
>>> Note that this is documented in the astropy.units.quantity section of
>>> the astropy documentation:
>>> http://docs.astropy.org/en/latest/units/quantity.html#converting-to-python-or-numpy-types
>>>
>>> Thanks,
>>> Adrian
>>>
>>> On Mar 21, 2013, at 2:20 PM, Jonathan Slavin wrote:
>>>
>>> > Hi,
>>> >
>>> > I have just used the constants module in astropy for the first time and
>>> > got 6 warnings from my code as a result:
>>> >
>>> > import astropy.constants as const
>>> > AU = const.au.to('km')
>>> >
>>> > leads to
>>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>>> > [astropy.units.quantity]
>>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>>> > [astropy.units.quantity]
>>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>>> > [astropy.units.quantity]
>>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>>> > [astropy.units.quantity]
>>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>>> > [astropy.units.quantity]
>>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>>> > [astropy.units.quantity]
>>> >
>>> > It seems that I get the warning every place I use the value of AU.  Do I
>>> > have to turn off warnings  to prevent this?  Is there some other way to
>>> > deal with this?
>>> >
>>> > Jon
>>> > --
>>> > ______________________________________________________________
>>> > Jonathan D. Slavin              Harvard-Smithsonian CfA
>>> > jslavin at cfa.harvard.edu         60 Garden Street, MS 83
>>> > phone: (617) 496-7981           Cambridge, MA 02138-1516
>>> > cell: (781) 363-0035           USA
>>> > ______________________________________________________________
>>> >
>>> > _______________________________________________
>>> > AstroPy mailing list
>>> > AstroPy at scipy.org
>>> > http://mail.scipy.org/mailman/listinfo/astropy
>>>
>>> --
>>> Adrian Price-Whelan
>>> Department of Astronomy
>>> Columbia University
>>>
>>>
>>>
>>
>> --
>> ______________________________________________________________
>> Jonathan D. Slavin              Harvard-Smithsonian CfA
>> jslavin at cfa.harvard.edu         60 Garden Street, MS 83
>> phone: (617) 496-7981           Cambridge, MA 02138-1516
>>  cell: (781) 363-0035           USA
>> ______________________________________________________________
>>
>> _______________________________________________
>> AstroPy mailing list
>> AstroPy at scipy.org
>> http://mail.scipy.org/mailman/listinfo/astropy
>
>
>
> --
> Erik Tollerud
> _______________________________________________
> AstroPy mailing list
> AstroPy at scipy.org
> http://mail.scipy.org/mailman/listinfo/astropy


From streetomon at gmail.com  Fri Mar 22 11:30:07 2013
From: streetomon at gmail.com (=?ISO-8859-1?Q?Andr=E9_Luiz_de_Amorim?=)
Date: Fri, 22 Mar 2013 16:30:07 +0100
Subject: [AstroPy] PyDev in danger of becoming unsupported
Message-ID: <CA+TxgtdJWx+jDkQaS_g13RSqGCfzm0LytkGp=JFJttcDsDSAgQ@mail.gmail.com>

Hi All,

sorry to bother you in what may be regarded as spam, but I think this is an
important issue.

PyDev/eclipse is one of the most used IDEs for python development. It is
maintained mostly by only one guy, Fabio Zadrozny, who used to be backed by
some companies. The support by these companies has ended, and Fabio began a
fund raising for PyDev:

http://www.indiegogo.com/projects/pydev-and-liclipse-for-a-fast-sexy-and-dark-eclipse

Please help keeping this great tool alive. :)

Andr?.
-------------- next part --------------
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From thomas.robitaille at gmail.com  Fri Mar 22 11:51:21 2013
From: thomas.robitaille at gmail.com (Thomas Robitaille)
Date: Fri, 22 Mar 2013 16:51:21 +0100
Subject: [AstroPy] why the warning about Converting Quantity?
In-Reply-To: <CAGMHX_3vtgXiuLRJPh9RDhzH5F1sCj3+bLu163ZrT8kmQ4+eSw@mail.gmail.com>
References: <1363890037.4653.6.camel@shevek>
	<1F835E06-111A-4D79-B703-D08CE549D665@gmail.com>
	<1363893770.8743.12.camel@shevek>
	<CAARXUwWmhzPXSr8ieRw+7hwkuQaT8k4Yfm3OW=fLVAs7SGbSDw@mail.gmail.com>
	<CAGMHX_3vtgXiuLRJPh9RDhzH5F1sCj3+bLu163ZrT8kmQ4+eSw@mail.gmail.com>
Message-ID: <CAGMHX_0x3-TNiOsQAEuoOjkwcwRoN16txcryg52V=Ub4ipav+Q@mail.gmail.com>

This is actually an issue with the Quantity class, not constants
(Constant inherits the issue from Quantity). I've opened an issue to
keep track of it:

https://github.com/astropy/astropy/pull/899

with some initial code which *should* have fixed it, but doesn't, due
to a Numpy issue.

Cheers,
Tom


On 22 March 2013 16:18, Thomas Robitaille <thomas.robitaille at gmail.com> wrote:
> I think that
>
> In [4]: np.array([1,2,3]) * constants.au
> WARNING: Converting Quantity object in units 'm' to a Numpy array
> [astropy.units.quantity]
> Out[4]: array([  1.49597871e+11,   2.99195741e+11,   4.48793612e+11])
>
> is actually a bug, as this should return a Quantity (like it does for
> scalars). I'll submit a PR shortly.
>
> Cheers,
> Tom
>
> On 22 March 2013 15:57, Erik Tollerud <erik.tollerud at gmail.com> wrote:
>> Hello Jonathan et al.,
>>
>> I think some confusion here stems from the fact that ``AU`` is a bit
>> of a special constant - in most cases, you're probably better off
>> using the AU *unit*, rather than the constant.  That is, if you were
>> doing something like
>>
>> arrinau = arr * constants.au
>>
>> That gives exactly the warning you mentioned, whereas
>>
>> arrinau = arr * units.au
>>
>> won't give out a warning, because it creates a `Quantity` object with
>> the units `AU`, rather than a regular array without any units.
>>
>>
>> Does that make sense, or am I still misunderstanding how you're using
>> this? If the latter, can you give an actual example of the line that
>> actually produces this warning? That'll make it easier to understand
>> exactly what you're suggesting.
>>
>>
>>
>>
>> On Thu, Mar 21, 2013 at 3:22 PM, Jonathan Slavin
>> <jslavin at cfa.harvard.edu> wrote:
>>> Hi Adrian,
>>>
>>> Yes, as I mentioned farther down in my post, the warnings are generated
>>> when I use it in an expression -- with numpy arrays.  It'd be nice to
>>> have a less cumbersome way of suppressing those warnings (yes it's just
>>> one line, but not so easy to remember).  In fact, I would expect to use
>>> the constants mostly in expressions with numpy arrays, variables, etc.
>>> that don't have units, so my preference would be that by default those
>>> warnings are turned off -- at least for the constants.  The constants
>>> are useful for their values alone, though clearly the value of the units
>>> module is to associate units with values.  Maybe a simple method like
>>> value.asfloat() could be added that would allow conversion from a units
>>> object to a numpy float.
>>>
>>> Jon
>>>
>>> On Thu, 2013-03-21 at 15:05 -0400, Adrian Price-Whelan wrote:
>>>> Hey Jonathan --
>>>>
>>>> Are you sure that's the point in the code that's producing the
>>>> warning? What operations are you doing with the AU object? When you
>>>> use the .to() method, it still returns a Quantity object -- *not* the
>>>> value of the original object in those units. If you then stick AU into
>>>> any numpy function, it will work but will just extract the value from
>>>> the object (hence the warning).
>>>>
>>>> See, for example:
>>>>
>>>> >>> import astropy.units as u
>>>> >>> np.sqrt(15*u.km)
>>>> WARNING: Converting Quantity object in units 'km' to a Numpy array
>>>> [astropy.units.quantity]
>>>> 3.872983346207417
>>>>
>>>> To turn this off, you'll want to set:
>>>> >>> u.quantity.WARN_IMPLICIT_NUMERIC_CONVERSION.set(False)
>>>> >>> np.sqrt(15*u.km)
>>>> 3.872983346207417
>>>>
>>>> Note that this is documented in the astropy.units.quantity section of
>>>> the astropy documentation:
>>>> http://docs.astropy.org/en/latest/units/quantity.html#converting-to-python-or-numpy-types
>>>>
>>>> Thanks,
>>>> Adrian
>>>>
>>>> On Mar 21, 2013, at 2:20 PM, Jonathan Slavin wrote:
>>>>
>>>> > Hi,
>>>> >
>>>> > I have just used the constants module in astropy for the first time and
>>>> > got 6 warnings from my code as a result:
>>>> >
>>>> > import astropy.constants as const
>>>> > AU = const.au.to('km')
>>>> >
>>>> > leads to
>>>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>>>> > [astropy.units.quantity]
>>>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>>>> > [astropy.units.quantity]
>>>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>>>> > [astropy.units.quantity]
>>>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>>>> > [astropy.units.quantity]
>>>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>>>> > [astropy.units.quantity]
>>>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>>>> > [astropy.units.quantity]
>>>> >
>>>> > It seems that I get the warning every place I use the value of AU.  Do I
>>>> > have to turn off warnings  to prevent this?  Is there some other way to
>>>> > deal with this?
>>>> >
>>>> > Jon
>>>> > --
>>>> > ______________________________________________________________
>>>> > Jonathan D. Slavin              Harvard-Smithsonian CfA
>>>> > jslavin at cfa.harvard.edu         60 Garden Street, MS 83
>>>> > phone: (617) 496-7981           Cambridge, MA 02138-1516
>>>> > cell: (781) 363-0035           USA
>>>> > ______________________________________________________________
>>>> >
>>>> > _______________________________________________
>>>> > AstroPy mailing list
>>>> > AstroPy at scipy.org
>>>> > http://mail.scipy.org/mailman/listinfo/astropy
>>>>
>>>> --
>>>> Adrian Price-Whelan
>>>> Department of Astronomy
>>>> Columbia University
>>>>
>>>>
>>>>
>>>
>>> --
>>> ______________________________________________________________
>>> Jonathan D. Slavin              Harvard-Smithsonian CfA
>>> jslavin at cfa.harvard.edu         60 Garden Street, MS 83
>>> phone: (617) 496-7981           Cambridge, MA 02138-1516
>>>  cell: (781) 363-0035           USA
>>> ______________________________________________________________
>>>
>>> _______________________________________________
>>> AstroPy mailing list
>>> AstroPy at scipy.org
>>> http://mail.scipy.org/mailman/listinfo/astropy
>>
>>
>>
>> --
>> Erik
>>
>> On Thu, Mar 21, 2013 at 3:22 PM, Jonathan Slavin
>> <jslavin at cfa.harvard.edu> wrote:
>>> Hi Adrian,
>>>
>>> Yes, as I mentioned farther down in my post, the warnings are generated
>>> when I use it in an expression -- with numpy arrays.  It'd be nice to
>>> have a less cumbersome way of suppressing those warnings (yes it's just
>>> one line, but not so easy to remember).  In fact, I would expect to use
>>> the constants mostly in expressions with numpy arrays, variables, etc.
>>> that don't have units, so my preference would be that by default those
>>> warnings are turned off -- at least for the constants.  The constants
>>> are useful for their values alone, though clearly the value of the units
>>> module is to associate units with values.  Maybe a simple method like
>>> value.asfloat() could be added that would allow conversion from a units
>>> object to a numpy float.
>>>
>>> Jon
>>>
>>> On Thu, 2013-03-21 at 15:05 -0400, Adrian Price-Whelan wrote:
>>>> Hey Jonathan --
>>>>
>>>> Are you sure that's the point in the code that's producing the
>>>> warning? What operations are you doing with the AU object? When you
>>>> use the .to() method, it still returns a Quantity object -- *not* the
>>>> value of the original object in those units. If you then stick AU into
>>>> any numpy function, it will work but will just extract the value from
>>>> the object (hence the warning).
>>>>
>>>> See, for example:
>>>>
>>>> >>> import astropy.units as u
>>>> >>> np.sqrt(15*u.km)
>>>> WARNING: Converting Quantity object in units 'km' to a Numpy array
>>>> [astropy.units.quantity]
>>>> 3.872983346207417
>>>>
>>>> To turn this off, you'll want to set:
>>>> >>> u.quantity.WARN_IMPLICIT_NUMERIC_CONVERSION.set(False)
>>>> >>> np.sqrt(15*u.km)
>>>> 3.872983346207417
>>>>
>>>> Note that this is documented in the astropy.units.quantity section of
>>>> the astropy documentation:
>>>> http://docs.astropy.org/en/latest/units/quantity.html#converting-to-python-or-numpy-types
>>>>
>>>> Thanks,
>>>> Adrian
>>>>
>>>> On Mar 21, 2013, at 2:20 PM, Jonathan Slavin wrote:
>>>>
>>>> > Hi,
>>>> >
>>>> > I have just used the constants module in astropy for the first time and
>>>> > got 6 warnings from my code as a result:
>>>> >
>>>> > import astropy.constants as const
>>>> > AU = const.au.to('km')
>>>> >
>>>> > leads to
>>>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>>>> > [astropy.units.quantity]
>>>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>>>> > [astropy.units.quantity]
>>>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>>>> > [astropy.units.quantity]
>>>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>>>> > [astropy.units.quantity]
>>>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>>>> > [astropy.units.quantity]
>>>> > WARNING: Converting Quantity object in units 'km' to a Numpy array
>>>> > [astropy.units.quantity]
>>>> >
>>>> > It seems that I get the warning every place I use the value of AU.  Do I
>>>> > have to turn off warnings  to prevent this?  Is there some other way to
>>>> > deal with this?
>>>> >
>>>> > Jon
>>>> > --
>>>> > ______________________________________________________________
>>>> > Jonathan D. Slavin              Harvard-Smithsonian CfA
>>>> > jslavin at cfa.harvard.edu         60 Garden Street, MS 83
>>>> > phone: (617) 496-7981           Cambridge, MA 02138-1516
>>>> > cell: (781) 363-0035           USA
>>>> > ______________________________________________________________
>>>> >
>>>> > _______________________________________________
>>>> > AstroPy mailing list
>>>> > AstroPy at scipy.org
>>>> > http://mail.scipy.org/mailman/listinfo/astropy
>>>>
>>>> --
>>>> Adrian Price-Whelan
>>>> Department of Astronomy
>>>> Columbia University
>>>>
>>>>
>>>>
>>>
>>> --
>>> ______________________________________________________________
>>> Jonathan D. Slavin              Harvard-Smithsonian CfA
>>> jslavin at cfa.harvard.edu         60 Garden Street, MS 83
>>> phone: (617) 496-7981           Cambridge, MA 02138-1516
>>>  cell: (781) 363-0035           USA
>>> ______________________________________________________________
>>>
>>> _______________________________________________
>>> AstroPy mailing list
>>> AstroPy at scipy.org
>>> http://mail.scipy.org/mailman/listinfo/astropy
>>
>>
>>
>> --
>> Erik Tollerud
>> _______________________________________________
>> AstroPy mailing list
>> AstroPy at scipy.org
>> http://mail.scipy.org/mailman/listinfo/astropy


From jslavin at cfa.harvard.edu  Fri Mar 22 12:32:59 2013
From: jslavin at cfa.harvard.edu (Jonathan Slavin)
Date: Fri, 22 Mar 2013 12:32:59 -0400
Subject: [AstroPy] why the warning about Converting Quantity?
In-Reply-To: <CAARXUwWmhzPXSr8ieRw+7hwkuQaT8k4Yfm3OW=fLVAs7SGbSDw@mail.gmail.com>
References: <1363890037.4653.6.camel@shevek>
	<1F835E06-111A-4D79-B703-D08CE549D665@gmail.com>
	<1363893770.8743.12.camel@shevek>
	<CAARXUwWmhzPXSr8ieRw+7hwkuQaT8k4Yfm3OW=fLVAs7SGbSDw@mail.gmail.com>
Message-ID: <1363969979.10525.80.camel@shevek>

Hi Erik,

In my case I'm actually using AU to convert from data that was returned
from another routine and has units of km to AU (the data are numpy
arrays.) e.g. 

AU = constants.au.to('km') 
xe = xem/AU # xem is in km, I want xe in AU

I could give xem the units of km in this example, though in fact the
actual expressions are a bit more complicated, but I just wanted to use
the constant value without bothering to look it up.  So I'm not, in this
instance, wanting to take advantage of the object's associated units
checking.  I think that that should not be so difficult.  Often one will
not want to bother to convert all one's data arrays to Quantity objects.
As I said, the constants are convenient for their values as well as the
units checking and it doesn't seem so unlikely that many would like to
use those values in contexts in which they won't want to bother to
define the units of all the other data.

Jon

On Fri, 2013-03-22 at 10:57 -0400, Erik Tollerud wrote:
> Hello Jonathan et al.,
> 
> I think some confusion here stems from the fact that ``AU`` is a bit
> of a special constant - in most cases, you're probably better off
> using the AU *unit*, rather than the constant.  That is, if you were
> doing something like
> 
> arrinau = arr * constants.au
> 
> That gives exactly the warning you mentioned, whereas
> 
> arrinau = arr * units.au
> 
> won't give out a warning, because it creates a `Quantity` object with
> the units `AU`, rather than a regular array without any units.
> 
> 
> Does that make sense, or am I still misunderstanding how you're using
> this? If the latter, can you give an actual example of the line that
> actually produces this warning? That'll make it easier to understand
> exactly what you're suggesting.
-- 
______________________________________________________________
Jonathan D. Slavin              Harvard-Smithsonian CfA
jslavin at cfa.harvard.edu         60 Garden Street, MS 83
phone: (617) 496-7981           Cambridge, MA 02138-1516
 cell: (781) 363-0035           USA
______________________________________________________________



From jslavin at cfa.harvard.edu  Fri Mar 22 12:37:51 2013
From: jslavin at cfa.harvard.edu (Jonathan Slavin)
Date: Fri, 22 Mar 2013 12:37:51 -0400
Subject: [AstroPy] why the warning about Converting Quantity?
In-Reply-To: <CAARXUwWmhzPXSr8ieRw+7hwkuQaT8k4Yfm3OW=fLVAs7SGbSDw@mail.gmail.com>
References: <1363890037.4653.6.camel@shevek>
	<1F835E06-111A-4D79-B703-D08CE549D665@gmail.com>
	<1363893770.8743.12.camel@shevek>
	<CAARXUwWmhzPXSr8ieRw+7hwkuQaT8k4Yfm3OW=fLVAs7SGbSDw@mail.gmail.com>
Message-ID: <1363970271.10525.82.camel@shevek>

Ah! Now I see.  All I needed to do was:

AU = constants.au.to('km').value
xe = xem/AU

By just using the value attribute I get what I want.

Jon

On Fri, 2013-03-22 at 10:57 -0400, Erik Tollerud wrote:
> Hello Jonathan et al.,
> 
> I think some confusion here stems from the fact that ``AU`` is a bit
> of a special constant - in most cases, you're probably better off
> using the AU *unit*, rather than the constant.  That is, if you were
> doing something like
> 
> arrinau = arr * constants.au
> 
> That gives exactly the warning you mentioned, whereas
> 
> arrinau = arr * units.au
> 
> won't give out a warning, because it creates a `Quantity` object with
> the units `AU`, rather than a regular array without any units.
> 
> 
> Does that make sense, or am I still misunderstanding how you're using
> this? If the latter, can you give an actual example of the line that
> actually produces this warning? That'll make it easier to understand
> exactly what you're suggesting.
> 
> 
> 
> 
> On Thu, Mar 21, 2013 at 3:22 PM, Jonathan Slavin
> <jslavin at cfa.harvard.edu> wrote:
> > Hi Adrian,
> >
> > Yes, as I mentioned farther down in my post, the warnings are generated
> > when I use it in an expression -- with numpy arrays.  It'd be nice to
> > have a less cumbersome way of suppressing those warnings (yes it's just
> > one line, but not so easy to remember).  In fact, I would expect to use
> > the constants mostly in expressions with numpy arrays, variables, etc.
> > that don't have units, so my preference would be that by default those
> > warnings are turned off -- at least for the constants.  The constants
> > are useful for their values alone, though clearly the value of the units
> > module is to associate units with values.  Maybe a simple method like
> > value.asfloat() could be added that would allow conversion from a units
> > object to a numpy float.
> >
> > Jon
> >
> > On Thu, 2013-03-21 at 15:05 -0400, Adrian Price-Whelan wrote:
> >> Hey Jonathan --
> >>
> >> Are you sure that's the point in the code that's producing the
> >> warning? What operations are you doing with the AU object? When you
> >> use the .to() method, it still returns a Quantity object -- *not* the
> >> value of the original object in those units. If you then stick AU into
> >> any numpy function, it will work but will just extract the value from
> >> the object (hence the warning).
> >>
> >> See, for example:
> >>
> >> >>> import astropy.units as u
> >> >>> np.sqrt(15*u.km)
> >> WARNING: Converting Quantity object in units 'km' to a Numpy array
> >> [astropy.units.quantity]
> >> 3.872983346207417
> >>
> >> To turn this off, you'll want to set:
> >> >>> u.quantity.WARN_IMPLICIT_NUMERIC_CONVERSION.set(False)
> >> >>> np.sqrt(15*u.km)
> >> 3.872983346207417
> >>
> >> Note that this is documented in the astropy.units.quantity section of
> >> the astropy documentation:
> >> http://docs.astropy.org/en/latest/units/quantity.html#converting-to-python-or-numpy-types
> >>
> >> Thanks,
> >> Adrian
> >>
> >> On Mar 21, 2013, at 2:20 PM, Jonathan Slavin wrote:
> >>
> >> > Hi,
> >> >
> >> > I have just used the constants module in astropy for the first time and
> >> > got 6 warnings from my code as a result:
> >> >
> >> > import astropy.constants as const
> >> > AU = const.au.to('km')
> >> >
> >> > leads to
> >> > WARNING: Converting Quantity object in units 'km' to a Numpy array
> >> > [astropy.units.quantity]
> >> > WARNING: Converting Quantity object in units 'km' to a Numpy array
> >> > [astropy.units.quantity]
> >> > WARNING: Converting Quantity object in units 'km' to a Numpy array
> >> > [astropy.units.quantity]
> >> > WARNING: Converting Quantity object in units 'km' to a Numpy array
> >> > [astropy.units.quantity]
> >> > WARNING: Converting Quantity object in units 'km' to a Numpy array
> >> > [astropy.units.quantity]
> >> > WARNING: Converting Quantity object in units 'km' to a Numpy array
> >> > [astropy.units.quantity]
> >> >
> >> > It seems that I get the warning every place I use the value of AU.  Do I
> >> > have to turn off warnings  to prevent this?  Is there some other way to
> >> > deal with this?
> >> >
> >> > Jon
> >> > --
> >> > ______________________________________________________________
> >> > Jonathan D. Slavin              Harvard-Smithsonian CfA
> >> > jslavin at cfa.harvard.edu         60 Garden Street, MS 83
> >> > phone: (617) 496-7981           Cambridge, MA 02138-1516
> >> > cell: (781) 363-0035           USA
> >> > ______________________________________________________________
> >> >
> >> > _______________________________________________
> >> > AstroPy mailing list
> >> > AstroPy at scipy.org
> >> > http://mail.scipy.org/mailman/listinfo/astropy
> >>
> >> --
> >> Adrian Price-Whelan
> >> Department of Astronomy
> >> Columbia University
> >>
> >>
> >>
> >
> > --
> > ______________________________________________________________
> > Jonathan D. Slavin              Harvard-Smithsonian CfA
> > jslavin at cfa.harvard.edu         60 Garden Street, MS 83
> > phone: (617) 496-7981           Cambridge, MA 02138-1516
> >  cell: (781) 363-0035           USA
> > ______________________________________________________________
> >
> > _______________________________________________
> > AstroPy mailing list
> > AstroPy at scipy.org
> > http://mail.scipy.org/mailman/listinfo/astropy
> 
> 
> 
> --
> Erik
> 
> On Thu, Mar 21, 2013 at 3:22 PM, Jonathan Slavin
> <jslavin at cfa.harvard.edu> wrote:
> > Hi Adrian,
> >
> > Yes, as I mentioned farther down in my post, the warnings are generated
> > when I use it in an expression -- with numpy arrays.  It'd be nice to
> > have a less cumbersome way of suppressing those warnings (yes it's just
> > one line, but not so easy to remember).  In fact, I would expect to use
> > the constants mostly in expressions with numpy arrays, variables, etc.
> > that don't have units, so my preference would be that by default those
> > warnings are turned off -- at least for the constants.  The constants
> > are useful for their values alone, though clearly the value of the units
> > module is to associate units with values.  Maybe a simple method like
> > value.asfloat() could be added that would allow conversion from a units
> > object to a numpy float.
> >
> > Jon
> >
> > On Thu, 2013-03-21 at 15:05 -0400, Adrian Price-Whelan wrote:
> >> Hey Jonathan --
> >>
> >> Are you sure that's the point in the code that's producing the
> >> warning? What operations are you doing with the AU object? When you
> >> use the .to() method, it still returns a Quantity object -- *not* the
> >> value of the original object in those units. If you then stick AU into
> >> any numpy function, it will work but will just extract the value from
> >> the object (hence the warning).
> >>
> >> See, for example:
> >>
> >> >>> import astropy.units as u
> >> >>> np.sqrt(15*u.km)
> >> WARNING: Converting Quantity object in units 'km' to a Numpy array
> >> [astropy.units.quantity]
> >> 3.872983346207417
> >>
> >> To turn this off, you'll want to set:
> >> >>> u.quantity.WARN_IMPLICIT_NUMERIC_CONVERSION.set(False)
> >> >>> np.sqrt(15*u.km)
> >> 3.872983346207417
> >>
> >> Note that this is documented in the astropy.units.quantity section of
> >> the astropy documentation:
> >> http://docs.astropy.org/en/latest/units/quantity.html#converting-to-python-or-numpy-types
> >>
> >> Thanks,
> >> Adrian
> >>
> >> On Mar 21, 2013, at 2:20 PM, Jonathan Slavin wrote:
> >>
> >> > Hi,
> >> >
> >> > I have just used the constants module in astropy for the first time and
> >> > got 6 warnings from my code as a result:
> >> >
> >> > import astropy.constants as const
> >> > AU = const.au.to('km')
> >> >
> >> > leads to
> >> > WARNING: Converting Quantity object in units 'km' to a Numpy array
> >> > [astropy.units.quantity]
> >> > WARNING: Converting Quantity object in units 'km' to a Numpy array
> >> > [astropy.units.quantity]
> >> > WARNING: Converting Quantity object in units 'km' to a Numpy array
> >> > [astropy.units.quantity]
> >> > WARNING: Converting Quantity object in units 'km' to a Numpy array
> >> > [astropy.units.quantity]
> >> > WARNING: Converting Quantity object in units 'km' to a Numpy array
> >> > [astropy.units.quantity]
> >> > WARNING: Converting Quantity object in units 'km' to a Numpy array
> >> > [astropy.units.quantity]
> >> >
> >> > It seems that I get the warning every place I use the value of AU.  Do I
> >> > have to turn off warnings  to prevent this?  Is there some other way to
> >> > deal with this?
> >> >
> >> > Jon
> >> > --
> >> > ______________________________________________________________
> >> > Jonathan D. Slavin              Harvard-Smithsonian CfA
> >> > jslavin at cfa.harvard.edu         60 Garden Street, MS 83
> >> > phone: (617) 496-7981           Cambridge, MA 02138-1516
> >> > cell: (781) 363-0035           USA
> >> > ______________________________________________________________
> >> >
> >> > _______________________________________________
> >> > AstroPy mailing list
> >> > AstroPy at scipy.org
> >> > http://mail.scipy.org/mailman/listinfo/astropy
> >>
> >> --
> >> Adrian Price-Whelan
> >> Department of Astronomy
> >> Columbia University
> >>
> >>
> >>
> >
> > --
> > ______________________________________________________________
> > Jonathan D. Slavin              Harvard-Smithsonian CfA
> > jslavin at cfa.harvard.edu         60 Garden Street, MS 83
> > phone: (617) 496-7981           Cambridge, MA 02138-1516
> >  cell: (781) 363-0035           USA
> > ______________________________________________________________
> >
> > _______________________________________________
> > AstroPy mailing list
> > AstroPy at scipy.org
> > http://mail.scipy.org/mailman/listinfo/astropy
> 
> 
> 
> --
> Erik Tollerud

-- 
______________________________________________________________
Jonathan D. Slavin              Harvard-Smithsonian CfA
jslavin at cfa.harvard.edu         60 Garden Street, MS 83
phone: (617) 496-7981           Cambridge, MA 02138-1516
 cell: (781) 363-0035           USA
______________________________________________________________



From embray at stsci.edu  Fri Mar 22 13:54:41 2013
From: embray at stsci.edu (Erik Bray)
Date: Fri, 22 Mar 2013 13:54:41 -0400
Subject: [AstroPy] why the warning about Converting Quantity?
In-Reply-To: <1363893770.8743.12.camel@shevek>
References: <1363890037.4653.6.camel@shevek>
	<1F835E06-111A-4D79-B703-D08CE549D665@gmail.com>
	<1363893770.8743.12.camel@shevek>
Message-ID: <514C9AE1.6080704@stsci.edu>

Hi Jon,

Since nobody else mentioned this I'll chime in.  You asked "it'd be nice to have 
a less cumbersome way of suppressing those warnings".  The 
u.quantity.WARN_IMPLICIT_NUMERIC_CONVERSION flag that Adrian mentioned is a 
configuration option which can be set permanently in your astropy.cfg file.  See 
http://astropy.readthedocs.org/en/latest/configs/index.html#using-config 
(although admittedly this is non-obvious; perhaps there's still room for 
improvement in the configuration docs for end-users).

In short, find your ~/.astropy/config/astropy.cfg and add

[units.quantity]
warn_implicit_numeric_conversion = False

to permanently disable this warning.  But remember, that places the onus on you 
to be careful about units when converting to types that don't carry the units 
with them (such as Numpy arrays).

Erik

On 03/21/2013 03:22 PM, Jonathan Slavin wrote:
> Hi Adrian,
>
> Yes, as I mentioned farther down in my post, the warnings are generated
> when I use it in an expression -- with numpy arrays.  It'd be nice to
> have a less cumbersome way of suppressing those warnings (yes it's just
> one line, but not so easy to remember).  In fact, I would expect to use
> the constants mostly in expressions with numpy arrays, variables, etc.
> that don't have units, so my preference would be that by default those
> warnings are turned off -- at least for the constants.  The constants
> are useful for their values alone, though clearly the value of the units
> module is to associate units with values.  Maybe a simple method like
> value.asfloat() could be added that would allow conversion from a units
> object to a numpy float.
>
> Jon
>
> On Thu, 2013-03-21 at 15:05 -0400, Adrian Price-Whelan wrote:
>> Hey Jonathan --
>>
>> Are you sure that's the point in the code that's producing the
>> warning? What operations are you doing with the AU object? When you
>> use the .to() method, it still returns a Quantity object -- *not* the
>> value of the original object in those units. If you then stick AU into
>> any numpy function, it will work but will just extract the value from
>> the object (hence the warning).
>>
>> See, for example:
>>
>>>>> import astropy.units as u
>>>>> np.sqrt(15*u.km)
>> WARNING: Converting Quantity object in units 'km' to a Numpy array
>> [astropy.units.quantity]
>> 3.872983346207417
>>
>> To turn this off, you'll want to set:
>>>>> u.quantity.WARN_IMPLICIT_NUMERIC_CONVERSION.set(False)
>>>>> np.sqrt(15*u.km)
>> 3.872983346207417
>>
>> Note that this is documented in the astropy.units.quantity section of
>> the astropy documentation:
>> http://docs.astropy.org/en/latest/units/quantity.html#converting-to-python-or-numpy-types
>>
>> Thanks,
>> Adrian
>>
>> On Mar 21, 2013, at 2:20 PM, Jonathan Slavin wrote:
>>
>>> Hi,
>>>
>>> I have just used the constants module in astropy for the first time and
>>> got 6 warnings from my code as a result:
>>>
>>> import astropy.constants as const
>>> AU = const.au.to('km')
>>>
>>> leads to
>>> WARNING: Converting Quantity object in units 'km' to a Numpy array
>>> [astropy.units.quantity]
>>> WARNING: Converting Quantity object in units 'km' to a Numpy array
>>> [astropy.units.quantity]
>>> WARNING: Converting Quantity object in units 'km' to a Numpy array
>>> [astropy.units.quantity]
>>> WARNING: Converting Quantity object in units 'km' to a Numpy array
>>> [astropy.units.quantity]
>>> WARNING: Converting Quantity object in units 'km' to a Numpy array
>>> [astropy.units.quantity]
>>> WARNING: Converting Quantity object in units 'km' to a Numpy array
>>> [astropy.units.quantity]
>>>
>>> It seems that I get the warning every place I use the value of AU.  Do I
>>> have to turn off warnings  to prevent this?  Is there some other way to
>>> deal with this?
>>>
>>> Jon
>>> --
>>> ______________________________________________________________
>>> Jonathan D. Slavin              Harvard-Smithsonian CfA
>>> jslavin at cfa.harvard.edu         60 Garden Street, MS 83
>>> phone: (617) 496-7981           Cambridge, MA 02138-1516
>>> cell: (781) 363-0035           USA
>>> ______________________________________________________________
>>>
>>> _______________________________________________
>>> AstroPy mailing list
>>> AstroPy at scipy.org
>>> http://mail.scipy.org/mailman/listinfo/astropy
>>
>> --
>> Adrian Price-Whelan
>> Department of Astronomy
>> Columbia University
>>
>>
>>
>



From aldcroft at head.cfa.harvard.edu  Mon Mar 25 12:46:51 2013
From: aldcroft at head.cfa.harvard.edu (Tom Aldcroft)
Date: Mon, 25 Mar 2013 12:46:51 -0400
Subject: [AstroPy] Dropping support for Numpy 1.4 in astropy
Message-ID: <CAGsQ-NsZ3QBg2TZj+4eqZ8jf5++FguEX7=gt69j_ZCVZ9fLv1Q@mail.gmail.com>

The Astropy project (http://astropy.org) is considering dropping
support for Numpy 1.4 in the next (0.3) release.  Drivers include:

- Masked arrays in 1.4 have a number of issues so that the astropy
Table class does not support missing values in numpy 1.4.
- Travis-CI cannot build numpy 1.4, so testing this configuration is
more difficult.
- Numpy 1.4 doesn't build easily on new platforms like Fedora 18.
- Numpy 1.7 (and soon 1.7.1) is out, so supporting the most recent 3
releases seems sufficient.

If anyone has any objections please raise them now.

Cheers,
Tom A


From ghang.naoc at gmail.com  Sun Mar 31 09:43:14 2013
From: ghang.naoc at gmail.com (gonghang.naoc)
Date: Sun, 31 Mar 2013 21:43:14 +0800
Subject: [AstroPy] HST photometry
Message-ID: <CABb23mvLMKsd__JG6OrE3D9_BoRMdvUVypTJgaK9jjudFG6B3A@mail.gmail.com>

Hi guys,

 Maybe it is not very relevant to the subject here.I am wondering anybody
ever done hst photometry here?I have read dolphot's manual but it is too
terse.Could anybody give me some quick help on the questions below?I have
downloaded c0m and c1m files from stsci.
    cosmic ray problem:There is  a command crrej and it has parameters like
dx and dy.The 2 parameters are powerful enough?We should align the images
before cosmic ray rejection?
If  one filter has more than one exposures we can combine the images to do
photometry.So it should be which step?After cosmic ray rejection?
    astrometry problem:It is the last step just before the workhorse of the
DOLPHOT package dolphot?DOLPHOT can not deal with that,right?Is there any
reliable python way to do that?

Any method except dolphot is welcome.

Thanks,

Hang
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