From sflarkin at ucsc.edu  Wed Apr  3 16:12:13 2019
From: sflarkin at ucsc.edu (Sean Larkin)
Date: Wed, 3 Apr 2019 13:12:13 -0700
Subject: [AstroPy] Question about Table Comments
Message-ID: <CADtuky==v6B-QAM+h8TkXJBR71V5u-tHsqVm8-uuhoCeJzCrmw@mail.gmail.com>

Hello all,

I have a question about the astropy.table comments attribute. I am
generating an table of the x, y, z and vx, vy, vz coordinates of particles
in a simulation to write to an ascii file to feed to another program for
analysis. The code I am using for this is as follows:

a_line = 'a = ' + scale_factor
comment = {'comments':[a_line]}

data = Table([x, y, z, vx, vy, vz, ids], names=['x', 'y', 'z', 'vx', 'vy',
'vz', 'id'], meta=comment)

 ascii.write(data, output=file_name)

The ascii file is written properly, with a format like:

# a = 0.21019612252712247

x y z vx vy vz id

4.112212871731752 3.778579779058581 4.11872852936419 -34.907225443016664
91.54097555566668 -140.89939877648789 0

4.112980377762908 3.778162574506875 4.1175911771358455 -35.195479563640525
91.50465485499448 -141.87647535372412 1


However, the program I am using expects comments in the form of :


#a = 0.21019612252712247


I am wondering if there is a way in astropy to remove the space between the
# and a in the comment when the file is written, or if there is another way
to add a comment like line of the above formatting.


Thank for your time and consideration!
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From derek at astro.physik.uni-goettingen.de  Wed Apr  3 16:25:44 2019
From: derek at astro.physik.uni-goettingen.de (Derek Homeier)
Date: Wed, 3 Apr 2019 22:25:44 +0200
Subject: [AstroPy] Question about Table Comments
In-Reply-To: <CADtuky==v6B-QAM+h8TkXJBR71V5u-tHsqVm8-uuhoCeJzCrmw@mail.gmail.com>
References: <CADtuky==v6B-QAM+h8TkXJBR71V5u-tHsqVm8-uuhoCeJzCrmw@mail.gmail.com>
Message-ID: <BFDB7BB7-22F9-403C-80AB-B76D64A665E1@astro.physik.uni-goettingen.de>

On 3 Apr 2019, at 10:12 pm, Sean Larkin <sflarkin at ucsc.edu> wrote:
> 
> I have a question about the astropy.table comments attribute. I am generating an table of the x, y, z and vx, vy, vz coordinates of particles in a simulation to write to an ascii file to feed to another program for analysis. The code I am using for this is as follows:
> 
> a_line = 'a = ' + scale_factor
> comment = {'comments':[a_line]}
>         
> data = Table([x, y, z, vx, vy, vz, ids], names=['x', 'y', 'z', 'vx', 'vy', 'vz', 'id'], meta=comment)
>         
>  ascii.write(data, output=file_name)
> 
> The ascii file is written properly, with a format like:
> 
> # a = 0.21019612252712247
> x y z vx vy vz id
> 4.112212871731752 3.778579779058581 4.11872852936419 -34.907225443016664 91.54097555566668 -140.89939877648789 0
> 4.112980377762908 3.778162574506875 4.1175911771358455 -35.195479563640525 91.50465485499448 -141.87647535372412 1
> 
> However, the program I am using expects comments in the form of :
> 
> #a = 0.21019612252712247
> 
> I am wondering if there is a way in astropy to remove the space between the # and a in the comment when the file is written, or if there is another way to add a comment like line of the above formatting.
> 
Have you tried to explicitly specify ascii.write(data, output=file_name, comment=?#?) ?
For me this is overriding the default write_comment=?# ?.

Cheers,
				Derek



From sflarkin at ucsc.edu  Wed Apr  3 16:32:55 2019
From: sflarkin at ucsc.edu (Sean Larkin)
Date: Wed, 3 Apr 2019 13:32:55 -0700
Subject: [AstroPy] Question about Table Comments
In-Reply-To: <BFDB7BB7-22F9-403C-80AB-B76D64A665E1@astro.physik.uni-goettingen.de>
References: <CADtuky==v6B-QAM+h8TkXJBR71V5u-tHsqVm8-uuhoCeJzCrmw@mail.gmail.com>
 <BFDB7BB7-22F9-403C-80AB-B76D64A665E1@astro.physik.uni-goettingen.de>
Message-ID: <CADtukymdLW83XsT2udw+YzqeSt-iipBP7v9U-CE0SZFHedBRLA@mail.gmail.com>

I had not tried that. I had initially tried:

ascii.write(data, output=file_name, comment=?#a = ...?)

believing that the comment in the ascii.write command was the same as in
the Table command. Thank you for the clarification, now it works exactly as
desired.

Thank you so much for the quick help!


On Wed, Apr 3, 2019 at 1:26 PM Derek Homeier <
derek at astro.physik.uni-goettingen.de> wrote:

> On 3 Apr 2019, at 10:12 pm, Sean Larkin <sflarkin at ucsc.edu> wrote:
> >
> > I have a question about the astropy.table comments attribute. I am
> generating an table of the x, y, z and vx, vy, vz coordinates of particles
> in a simulation to write to an ascii file to feed to another program for
> analysis. The code I am using for this is as follows:
> >
> > a_line = 'a = ' + scale_factor
> > comment = {'comments':[a_line]}
> >
> > data = Table([x, y, z, vx, vy, vz, ids], names=['x', 'y', 'z', 'vx',
> 'vy', 'vz', 'id'], meta=comment)
> >
> >  ascii.write(data, output=file_name)
> >
> > The ascii file is written properly, with a format like:
> >
> > # a = 0.21019612252712247
> > x y z vx vy vz id
> > 4.112212871731752 3.778579779058581 4.11872852936419 -34.907225443016664
> 91.54097555566668 -140.89939877648789 0
> > 4.112980377762908 3.778162574506875 4.1175911771358455
> -35.195479563640525 91.50465485499448 -141.87647535372412 1
> >
> > However, the program I am using expects comments in the form of :
> >
> > #a = 0.21019612252712247
> >
> > I am wondering if there is a way in astropy to remove the space between
> the # and a in the comment when the file is written, or if there is another
> way to add a comment like line of the above formatting.
> >
> Have you tried to explicitly specify ascii.write(data, output=file_name,
> comment=?#?) ?
> For me this is overriding the default write_comment=?# ?.
>
> Cheers,
>                                 Derek
>
>
> _______________________________________________
> AstroPy mailing list
> AstroPy at python.org
> https://mail.python.org/mailman/listinfo/astropy
>
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From adrianmpw at gmail.com  Tue Apr 16 11:58:00 2019
From: adrianmpw at gmail.com (Adrian Price-Whelan)
Date: Tue, 16 Apr 2019 08:58:00 -0700
Subject: [AstroPy] Gala v1.0 released
Message-ID: <CAEUL7mHO8c2z0gaRBHpA3R+xdZgJ=vHBnk-tgXgyz_hzC_Cw+w@mail.gmail.com>

Gala is an Astropy affiliated package for Galactic dynamics. Most of
its functionality centers around implementations of gravitational
potential models, numerical orbit integration, stellar stream
modeling, and nonlinear dynamics, and all works natively with
astropy.units and astropy.coordinates.

You can read more about Gala and see examples and tutorials in the
documentation:
http://gala.adrian.pw/en/stable/

v1.0 contains many new features, including:
- great circle coordinate frames that work with astropy coordinates
- new potential models, including MWPotential2014 from galpy
- SCF (basis function expansion) flexible potential representations
- new stellar stream coordinate frames
You can read more about these new features in the What's New documentation:
http://gala.adrian.pw/en/stable/whatsnew/1.0.html


To install or update the latest version (v1.0), you can use conda or
pip. For example:

conda install -c conda-forge astro-gala

or

pip install astro-gala

Please report and issues or suggest new features through the issue
tracker on GitHub:

https://github.com/adrn/gala/issues


thanks!
- Adrian

-- 
Adrian M. Price-Whelan
Lyman Spitzer, Jr. Postdoctoral Fellow
Princeton University
http://adrn.github.io

From hessman at astro.physik.uni-goettingen.de  Wed Apr 17 09:43:56 2019
From: hessman at astro.physik.uni-goettingen.de (Frederic V. Hessman)
Date: Wed, 17 Apr 2019 15:43:56 +0200
Subject: [AstroPy] HDU to Table
Message-ID: <1444AA35-E9B5-45F5-99FC-E2CFA5941D80@astro.physik.uni-goettingen.de>

There's the convenience function 

	astropy.io.fits.table_to_hdu (astropy.table.Table) -> astropy.io.fits.BinTableHDU

but where's 

	astropy.io.fits.hdu_to_table(astropy.io.fits.BinTableHDU) -> astropy.table.Table ?

Surely people are writing AND reading binary tables.....!    I want to dump IFU spectra into a single FITS binary table file and then easily read them back in again.

My internet searches haven't yielded anything equivalent.  Of course, one can write the reverse conversion (one can write anything/everything), but this should be a standard FITS/Table function.

Rick

------------------------------------------------------------------------------------------------
Dr. Frederic V. Hessman     Hessman at Astro.physik.Uni-Goettingen.DE
Institut f?r Astrophysik          Tel.  +49-551-39-5052
Friedrich-Hund-Platz 1         Fax +49-551-39-5043
37077 Goettingen                 Room F04-133
http://www.Astro.physik.Uni-Goettingen.de/~hessman
-------------------------------------------------------------------------------------------------
MONET: a MOnitoring NEtwork of Telescopes
http://monet.Uni-Goettingen.de
-------------------------------------------------------------------------------------------------



From bjw at as.arizona.edu  Wed Apr 17 12:51:48 2019
From: bjw at as.arizona.edu (Benjamin Weiner)
Date: Wed, 17 Apr 2019 09:51:48 -0700
Subject: [AstroPy] AstroPy Digest, Vol 151, Issue 3
In-Reply-To: <mailman.33.1555516803.7041.astropy@python.org>
References: <mailman.33.1555516803.7041.astropy@python.org>
Message-ID: <CAAKCKFFybJeLCx5qcVkc8w0SG0Vs5K3yY11=igFu2JvFD7s5CA@mail.gmail.com>

Hello Rick,

You should be able to read a FITS binary table with something like:

from astropy.io import fits
hdulist = fits.open('myfilename.fits')
mydata = hdu[1].data   # makes a table from the data in extension 1

This is covered in the astropy.io.fits documentation at
http://docs.astropy.org/en/stable/io/fits/

Cheers,
Ben Weiner

Date: Wed, 17 Apr 2019 15:43:56 +0200
> From: "Frederic V. Hessman" <hessman at astro.physik.uni-goettingen.de>
> To: astropy at python.org
> Subject: [AstroPy] HDU to Table
>
> There's the convenience function
>
>         astropy.io.fits.table_to_hdu (astropy.table.Table) ->
> astropy.io.fits.BinTableHDU
>
> but where's
>
>         astropy.io.fits.hdu_to_table(astropy.io.fits.BinTableHDU) ->
> astropy.table.Table ?
>
> Surely people are writing AND reading binary tables.....!    I want to
> dump IFU spectra into a single FITS binary table file and then easily read
> them back in again.
>
> My internet searches haven't yielded anything equivalent.  Of course, one
> can write the reverse conversion (one can write anything/everything), but
> this should be a standard FITS/Table function.
>
> Rick
>
>
> ------------------------------------------------------------------------------------------------
> Dr. Frederic V. Hessman     Hessman at Astro.physik.Uni-Goettingen.DE
> Institut f?r Astrophysik          Tel.  +49-551-39-5052
> Friedrich-Hund-Platz 1         Fax +49-551-39-5043
> 37077 Goettingen                 Room F04-133
> http://www.Astro.physik.Uni-Goettingen.de/~hessman
>
> -------------------------------------------------------------------------------------------------
> MONET: a MOnitoring NEtwork of Telescopes
> http://monet.Uni-Goettingen.de
>
> -------------------------------------------------------------------------------------------------
>
>
-- 
Benjamin Weiner
Staff Scientist / Associate Astronomer, MMT / Steward Observatory
bjw at as.arizona.edu
http://mingus.mmto.arizona.edu/~bjw/ <http://mingus.as.arizona.edu/~bjw/>
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From bjw at as.arizona.edu  Wed Apr 17 12:52:53 2019
From: bjw at as.arizona.edu (Benjamin Weiner)
Date: Wed, 17 Apr 2019 09:52:53 -0700
Subject: [AstroPy] AstroPy Digest, Vol 151, Issue 3
In-Reply-To: <CAAKCKFFybJeLCx5qcVkc8w0SG0Vs5K3yY11=igFu2JvFD7s5CA@mail.gmail.com>
References: <mailman.33.1555516803.7041.astropy@python.org>
 <CAAKCKFFybJeLCx5qcVkc8w0SG0Vs5K3yY11=igFu2JvFD7s5CA@mail.gmail.com>
Message-ID: <CAAKCKFHqEHdkdBhEwO7_XeDCSkOjaNwBwmXUe9NqZ7k9gtxoBA@mail.gmail.com>

Ugh, I mistyped a variable name, my example should be
hdulist = fits.open('myfilename.fits')
mydata = hdulist[1].data   # makes a table from the data in extension 1



On Wed, Apr 17, 2019 at 9:51 AM Benjamin Weiner <bjw at as.arizona.edu> wrote:

> Hello Rick,
>
> You should be able to read a FITS binary table with something like:
>
> from astropy.io import fits
> hdulist = fits.open('myfilename.fits')
> mydata = hdu[1].data   # makes a table from the data in extension 1
>
> This is covered in the astropy.io.fits documentation at
> http://docs.astropy.org/en/stable/io/fits/
>
> Cheers,
> Ben Weiner
>
> Date: Wed, 17 Apr 2019 15:43:56 +0200
>> From: "Frederic V. Hessman" <hessman at astro.physik.uni-goettingen.de>
>> To: astropy at python.org
>> Subject: [AstroPy] HDU to Table
>>
>> There's the convenience function
>>
>>         astropy.io.fits.table_to_hdu (astropy.table.Table) ->
>> astropy.io.fits.BinTableHDU
>>
>> but where's
>>
>>         astropy.io.fits.hdu_to_table(astropy.io.fits.BinTableHDU) ->
>> astropy.table.Table ?
>>
>> Surely people are writing AND reading binary tables.....!    I want to
>> dump IFU spectra into a single FITS binary table file and then easily read
>> them back in again.
>>
>> My internet searches haven't yielded anything equivalent.  Of course, one
>> can write the reverse conversion (one can write anything/everything), but
>> this should be a standard FITS/Table function.
>>
>> Rick
>>
>>
>> ------------------------------------------------------------------------------------------------
>> Dr. Frederic V. Hessman     Hessman at Astro.physik.Uni-Goettingen.DE
>> Institut f?r Astrophysik          Tel.  +49-551-39-5052
>> Friedrich-Hund-Platz 1         Fax +49-551-39-5043
>> 37077 Goettingen                 Room F04-133
>> http://www.Astro.physik.Uni-Goettingen.de/~hessman
>>
>> -------------------------------------------------------------------------------------------------
>> MONET: a MOnitoring NEtwork of Telescopes
>> http://monet.Uni-Goettingen.de
>>
>> -------------------------------------------------------------------------------------------------
>>
>>
> --
> Benjamin Weiner
> Staff Scientist / Associate Astronomer, MMT / Steward Observatory
> bjw at as.arizona.edu
> http://mingus.mmto.arizona.edu/~bjw/ <http://mingus.as.arizona.edu/~bjw/>
>


-- 
Benjamin Weiner
Staff Scientist / Associate Astronomer, MMT / Steward Observatory
bjw at as.arizona.edu
http://mingus.mmto.arizona.edu/~bjw/ <http://mingus.as.arizona.edu/~bjw/>
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From deil.christoph at googlemail.com  Wed Apr 17 13:41:20 2019
From: deil.christoph at googlemail.com (Christoph Deil)
Date: Wed, 17 Apr 2019 19:41:20 +0200
Subject: [AstroPy] AstroPy Digest, Vol 151, Issue 3
In-Reply-To: <CAAKCKFHqEHdkdBhEwO7_XeDCSkOjaNwBwmXUe9NqZ7k9gtxoBA@mail.gmail.com>
References: <mailman.33.1555516803.7041.astropy@python.org>
 <CAAKCKFFybJeLCx5qcVkc8w0SG0Vs5K3yY11=igFu2JvFD7s5CA@mail.gmail.com>
 <CAAKCKFHqEHdkdBhEwO7_XeDCSkOjaNwBwmXUe9NqZ7k9gtxoBA@mail.gmail.com>
Message-ID: <F50059BA-3079-44C8-8998-0A68B21B2202@googlemail.com>

Hi Rick,

if you want a astropy.table.Table object, use Table.read.

You can pass it a filename, but you can also pass an astropy.io <http://astropy.io/>.fits.BinTableHDU object,
If for some reason you already have it in memory.

I agree it?s weird that Table.read does this, adding a astropy.io.fits.hdu_to_table function would make this easier to discover.
Maybe file an issue with Astropy with that suggestion?

Christoph

> On 17. Apr 2019, at 18:52, Benjamin Weiner <bjw at as.arizona.edu> wrote:
> 
> Ugh, I mistyped a variable name, my example should be 
> hdulist = fits.open('myfilename.fits')
> mydata = hdulist[1].data   # makes a table from the data in extension 1
> 
> 
> 
> On Wed, Apr 17, 2019 at 9:51 AM Benjamin Weiner <bjw at as.arizona.edu <mailto:bjw at as.arizona.edu>> wrote:
> Hello Rick,
> 
> You should be able to read a FITS binary table with something like:
> 
> from astropy.io <http://astropy.io/> import fits
> hdulist = fits.open('myfilename.fits')
> mydata = hdu[1].data   # makes a table from the data in extension 1
> 
> This is covered in the astropy.io.fits documentation at http://docs.astropy.org/en/stable/io/fits/ <http://docs.astropy.org/en/stable/io/fits/>
> 
> Cheers,
> Ben Weiner
> 
> Date: Wed, 17 Apr 2019 15:43:56 +0200
> From: "Frederic V. Hessman" <hessman at astro.physik.uni-goettingen.de <mailto:hessman at astro.physik.uni-goettingen.de>>
> To: astropy at python.org <mailto:astropy at python.org>
> Subject: [AstroPy] HDU to Table
> 
> There's the convenience function 
> 
>         astropy.io.fits.table_to_hdu (astropy.table.Table) -> astropy.io.fits.BinTableHDU
> 
> but where's 
> 
>         astropy.io.fits.hdu_to_table(astropy.io.fits.BinTableHDU) -> astropy.table.Table ?
> 
> Surely people are writing AND reading binary tables.....!    I want to dump IFU spectra into a single FITS binary table file and then easily read them back in again.
> 
> My internet searches haven't yielded anything equivalent.  Of course, one can write the reverse conversion (one can write anything/everything), but this should be a standard FITS/Table function.
> 
> Rick
> 
> ------------------------------------------------------------------------------------------------
> Dr. Frederic V. Hessman     Hessman at Astro.physik.Uni-Goettingen.DE <mailto:Hessman at Astro.physik.Uni-Goettingen.DE>
> Institut f?r Astrophysik          Tel.  +49-551-39-5052
> Friedrich-Hund-Platz 1         Fax +49-551-39-5043
> 37077 Goettingen                 Room F04-133
> http://www.Astro.physik.Uni-Goettingen.de/~hessman <http://www.astro.physik.uni-goettingen.de/~hessman>
> -------------------------------------------------------------------------------------------------
> MONET: a MOnitoring NEtwork of Telescopes
> http://monet.Uni-Goettingen.de <http://monet.uni-goettingen.de/>
> -------------------------------------------------------------------------------------------------
> 
>  
> -- 
> Benjamin Weiner   
> Staff Scientist / Associate Astronomer, MMT / Steward Observatory
> bjw at as.arizona.edu <mailto:bjw at as.arizona.edu>
> http://mingus.mmto.arizona.edu/~bjw/ <http://mingus.as.arizona.edu/~bjw/>
> 
> 
> -- 
> Benjamin Weiner   
> Staff Scientist / Associate Astronomer, MMT / Steward Observatory
> bjw at as.arizona.edu <mailto:bjw at as.arizona.edu>
> http://mingus.mmto.arizona.edu/~bjw/ <http://mingus.as.arizona.edu/~bjw/>
> _______________________________________________
> AstroPy mailing list
> AstroPy at python.org <mailto:AstroPy at python.org>
> https://mail.python.org/mailman/listinfo/astropy <https://mail.python.org/mailman/listinfo/astropy>
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From ivvv68 at gmail.com  Wed Apr 17 14:32:16 2019
From: ivvv68 at gmail.com (Ivan Valtchanov)
Date: Wed, 17 Apr 2019 20:32:16 +0200
Subject: [AstroPy] AstroPy Digest, Vol 151, Issue 3
In-Reply-To: <F50059BA-3079-44C8-8998-0A68B21B2202@googlemail.com>
References: <mailman.33.1555516803.7041.astropy@python.org>
 <CAAKCKFFybJeLCx5qcVkc8w0SG0Vs5K3yY11=igFu2JvFD7s5CA@mail.gmail.com>
 <CAAKCKFHqEHdkdBhEwO7_XeDCSkOjaNwBwmXUe9NqZ7k9gtxoBA@mail.gmail.com>
 <F50059BA-3079-44C8-8998-0A68B21B2202@googlemail.com>
Message-ID: <CAHu8e_5OpLVZB0z=X4jAAAJFtArvkuTBdfhSOLeMHuJU8FW0PA@mail.gmail.com>

Hi Christoph,

You cannot use BinTableHDU to create an astropy.tableTable object. When you
try to do this you get this error:

table = Table(hdu[1])

 Data type <class 'astropy.io.fits.hdu.table.BinTableHDU'> not allowed to
init Table

But this one works,

table = Table(hdu[1].data)

although I don't think it's documented in  astropy.table docs.
<http://docs.astropy.org/en/stable/table/> I could not find it easily.

Cheers,
Ivan


On Wed, 17 Apr 2019 at 19:41, Christoph Deil <deil.christoph at googlemail.com>
wrote:

> Hi Rick,
>
> if you want a astropy.table.Table object, use Table.read.
>
> You can pass it a filename, but you can also pass an astropy.io.fits.BinTableHDU
> object,
> If for some reason you already have it in memory.
>
> I agree it?s weird that Table.read does this, adding a
> astropy.io.fits.hdu_to_table function would make this easier to discover.
> Maybe file an issue with Astropy with that suggestion?
>
> Christoph
>
> On 17. Apr 2019, at 18:52, Benjamin Weiner <bjw at as.arizona.edu> wrote:
>
> Ugh, I mistyped a variable name, my example should be
> hdulist = fits.open('myfilename.fits')
> mydata = hdulist[1].data   # makes a table from the data in extension 1
>
>
>
> On Wed, Apr 17, 2019 at 9:51 AM Benjamin Weiner <bjw at as.arizona.edu>
> wrote:
>
>> Hello Rick,
>>
>> You should be able to read a FITS binary table with something like:
>>
>> from astropy.io import fits
>> hdulist = fits.open('myfilename.fits')
>> mydata = hdu[1].data   # makes a table from the data in extension 1
>>
>> This is covered in the astropy.io.fits documentation at
>> http://docs.astropy.org/en/stable/io/fits/
>>
>> Cheers,
>> Ben Weiner
>>
>> Date: Wed, 17 Apr 2019 15:43:56 +0200
>>> From: "Frederic V. Hessman" <hessman at astro.physik.uni-goettingen.de>
>>> To: astropy at python.org
>>> Subject: [AstroPy] HDU to Table
>>>
>>> There's the convenience function
>>>
>>>         astropy.io.fits.table_to_hdu (astropy.table.Table) ->
>>> astropy.io.fits.BinTableHDU
>>>
>>> but where's
>>>
>>>         astropy.io.fits.hdu_to_table(astropy.io.fits.BinTableHDU) ->
>>> astropy.table.Table ?
>>>
>>> Surely people are writing AND reading binary tables.....!    I want to
>>> dump IFU spectra into a single FITS binary table file and then easily read
>>> them back in again.
>>>
>>> My internet searches haven't yielded anything equivalent.  Of course,
>>> one can write the reverse conversion (one can write anything/everything),
>>> but this should be a standard FITS/Table function.
>>>
>>> Rick
>>>
>>>
>>> ------------------------------------------------------------------------------------------------
>>> Dr. Frederic V. Hessman     Hessman at Astro.physik.Uni-Goettingen.DE
>>> Institut f?r Astrophysik          Tel.  +49-551-39-5052
>>> Friedrich-Hund-Platz 1         Fax +49-551-39-5043
>>> 37077 Goettingen                 Room F04-133
>>> http://www.Astro.physik.Uni-Goettingen.de/~hessman
>>> <http://www.astro.physik.uni-goettingen.de/~hessman>
>>>
>>> -------------------------------------------------------------------------------------------------
>>> MONET: a MOnitoring NEtwork of Telescopes
>>> http://monet.Uni-Goettingen.de <http://monet.uni-goettingen.de/>
>>>
>>> -------------------------------------------------------------------------------------------------
>>>
>>>
>> --
>> Benjamin Weiner
>> Staff Scientist / Associate Astronomer, MMT / Steward Observatory
>> bjw at as.arizona.edu
>> http://mingus.mmto.arizona.edu/~bjw/ <http://mingus.as.arizona.edu/~bjw/>
>>
>
>
> --
> Benjamin Weiner
> Staff Scientist / Associate Astronomer, MMT / Steward Observatory
> bjw at as.arizona.edu
> http://mingus.mmto.arizona.edu/~bjw/ <http://mingus.as.arizona.edu/~bjw/>
> _______________________________________________
> AstroPy mailing list
> AstroPy at python.org
> https://mail.python.org/mailman/listinfo/astropy
>
>
> _______________________________________________
> AstroPy mailing list
> AstroPy at python.org
> https://mail.python.org/mailman/listinfo/astropy
>
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From derek at astro.physik.uni-goettingen.de  Wed Apr 17 14:52:23 2019
From: derek at astro.physik.uni-goettingen.de (Derek Homeier)
Date: Wed, 17 Apr 2019 20:52:23 +0200
Subject: [AstroPy] AstroPy Digest - HDU to Table
In-Reply-To: <F50059BA-3079-44C8-8998-0A68B21B2202@googlemail.com>
References: <mailman.33.1555516803.7041.astropy@python.org>
 <CAAKCKFFybJeLCx5qcVkc8w0SG0Vs5K3yY11=igFu2JvFD7s5CA@mail.gmail.com>
 <CAAKCKFHqEHdkdBhEwO7_XeDCSkOjaNwBwmXUe9NqZ7k9gtxoBA@mail.gmail.com>
 <F50059BA-3079-44C8-8998-0A68B21B2202@googlemail.com>
Message-ID: <3D4ED4C0-C264-42BE-AD3F-25E33101A41F@astro.physik.uni-goettingen.de>

On 17 Apr 2019, at 7:41 pm, Christoph Deil <deil.christoph at googlemail.com> wrote:
> 
> if you want a astropy.table.Table object, use Table.read.
> 
> You can pass it a filename, but you can also pass an astropy.io.fits.BinTableHDU object,
> If for some reason you already have it in memory.
> 
> I agree it?s weird that Table.read does this, adding a astropy.io.fits.hdu_to_table function would make this easier to discover.
> Maybe file an issue with Astropy with that suggestion?
> 
Two small clarifications: direct Table initialisation requires the `data` part, e.g.

astropy.table.Table(binhdu.data)

but it still preserves structure and column names of the FITS table. If in addition you want to keep
the complete header information, you need to explicitly pass it to the table.meta data, i.e.

astropy.table.Table(binhdu.data, meta=binhdu.header)

so you may say this still requires a wrapper, but it?s a pretty thin one.

For reading from file I have to add that my understanding of the documentation 
http://docs.astropy.org/en/stable/io/unified.html#keywords
"The FITS keywords associated with an HDU table are represented in the meta ordered dictionary attribute of a Table. ?

is actually that Table.read(?filename.fits?, [hdu=n]) should do this automatically, but in fact,
just like Table() without the meta keyword it ends up with an empty dictionary in table.meta.

This looks indeed like a real issue (either fix the documentation, or better, implement the
functionality it describes).

Cheers,
					Derek


From derek at astro.physik.uni-goettingen.de  Wed Apr 17 18:41:40 2019
From: derek at astro.physik.uni-goettingen.de (Derek Homeier)
Date: Thu, 18 Apr 2019 00:41:40 +0200
Subject: [AstroPy] AstroPy Digest - HDU to Table
In-Reply-To: <3D4ED4C0-C264-42BE-AD3F-25E33101A41F@astro.physik.uni-goettingen.de>
References: <mailman.33.1555516803.7041.astropy@python.org>
 <CAAKCKFFybJeLCx5qcVkc8w0SG0Vs5K3yY11=igFu2JvFD7s5CA@mail.gmail.com>
 <CAAKCKFHqEHdkdBhEwO7_XeDCSkOjaNwBwmXUe9NqZ7k9gtxoBA@mail.gmail.com>
 <F50059BA-3079-44C8-8998-0A68B21B2202@googlemail.com>
 <3D4ED4C0-C264-42BE-AD3F-25E33101A41F@astro.physik.uni-goettingen.de>
Message-ID: <FF7BBAB3-7503-4CAE-9FE1-C9C38E5C0C55@astro.physik.uni-goettingen.de>

On 17 Apr 2019, at 8:52 pm, Derek Homeier <derek at astro.physik.uni-goettingen.de> wrote:
> 
> On 17 Apr 2019, at 7:41 pm, Christoph Deil <deil.christoph at googlemail.com> wrote:
>> 
>> if you want a astropy.table.Table object, use Table.read.
>> 
>> You can pass it a filename, but you can also pass an astropy.io.fits.BinTableHDU object,
>> If for some reason you already have it in memory.
>> 
>> I agree it?s weird that Table.read does this, adding a astropy.io.fits.hdu_to_table function would make this easier to discover.
>> Maybe file an issue with Astropy with that suggestion?
>> 
> Two small clarifications: direct Table initialisation requires the `data` part, e.g.
> 
> astropy.table.Table(binhdu.data)
> 
> but it still preserves structure and column names of the FITS table. If in addition you want to keep
> the complete header information, you need to explicitly pass it to the table.meta data, i.e.
> 
> astropy.table.Table(binhdu.data, meta=binhdu.header)
> 
> so you may say this still requires a wrapper, but it?s a pretty thin one.
> 
> For reading from file I have to add that my understanding of the documentation 
> http://docs.astropy.org/en/stable/io/unified.html#keywords
> "The FITS keywords associated with an HDU table are represented in the meta ordered dictionary attribute of a Table. ?
> 
> is actually that Table.read(?filename.fits?, [hdu=n]) should do this automatically, but in fact,
> just like Table() without the meta keyword it ends up with an empty dictionary in table.meta.
> 
I stand corrected here: Table.read() does store the header cards in the meta attribute,
after stripping the functional keywords defining the table itself and a couple of other blacklisted
cards - which just happened to be *all* of the cards in some of the test files in the distribution.
In contrast, this works as expected:

>>> chandra = Table.read('https://github.com/astropy/astropy/blob/master/astropy/io/fits/tests/data/chandra_time.fits?raw=true?)
>>> chandra.meta['TITLE']
Multiwavelength Characterization of Candidate Black Holes in Nearby Dwarf Galaxies

Cheers,
				Derek


From derek at astro.physik.uni-goettingen.de  Wed Apr 17 19:13:53 2019
From: derek at astro.physik.uni-goettingen.de (Derek Homeier)
Date: Thu, 18 Apr 2019 01:13:53 +0200
Subject: [AstroPy] AstroPy Digest, Vol 151, Issue 3
In-Reply-To: <CAHu8e_5OpLVZB0z=X4jAAAJFtArvkuTBdfhSOLeMHuJU8FW0PA@mail.gmail.com>
References: <mailman.33.1555516803.7041.astropy@python.org>
 <CAAKCKFFybJeLCx5qcVkc8w0SG0Vs5K3yY11=igFu2JvFD7s5CA@mail.gmail.com>
 <CAAKCKFHqEHdkdBhEwO7_XeDCSkOjaNwBwmXUe9NqZ7k9gtxoBA@mail.gmail.com>
 <F50059BA-3079-44C8-8998-0A68B21B2202@googlemail.com>
 <CAHu8e_5OpLVZB0z=X4jAAAJFtArvkuTBdfhSOLeMHuJU8FW0PA@mail.gmail.com>
Message-ID: <4586D712-70EA-4984-8C54-906D4B2813B2@astro.physik.uni-goettingen.de>

On 17 Apr 2019, at 8:32 pm, Ivan Valtchanov <ivvv68 at gmail.com> wrote:
> 
> You cannot use BinTableHDU to create an astropy.tableTable object. When you try to do this you get this error:
> 
> table = Table(hdu[1])
> 
>  Data type <class 'astropy.io.fits.hdu.table.BinTableHDU'> not allowed to init Table
> 
> But this one works,
> 
> table = Table(hdu[1].data) 
> 
> although I don't think it's documented in  astropy.table docs. I could not find it easily.
> 
Actually you can pass the BinTableHDU object to the read() function instead of a file,
which will properly handle the rest (including filling the table.meta information), and
that?s probably what Christoph referred to:

table = Table.read(hdu[1])

But it certainly looks like a peculiar egg; Happy Easter!

					Derek


From hessman at astro.physik.uni-goettingen.de  Thu Apr 18 03:44:04 2019
From: hessman at astro.physik.uni-goettingen.de (Frederic V. Hessman)
Date: Thu, 18 Apr 2019 09:44:04 +0200
Subject: [AstroPy] AstroPy Digest, Vol 151, Issue 5
In-Reply-To: <mailman.3356.1555540862.2981.astropy@python.org>
References: <mailman.3356.1555540862.2981.astropy@python.org>
Message-ID: <A9F5C910-FB8C-4477-909F-AEBD28AD8EBC@astro.physik.uni-goettingen.de>

Thanks for the various tips...

> But this one works,
> 
> table = Table(hdu[1].data)
> 
> although I don't think it's documented in  astropy.table docs.
> <http://docs.astropy.org/en/stable/table/> I could not find it easily.
> 
> Cheers,
> Ivan

> Two small clarifications: direct Table initialisation requires the `data` part, e.g.
> 
> astropy.table.Table(binhdu.data)
> 
> but it still preserves structure and column names of the FITS table.

Aha!  This is because np.ndarray has dtype.names!     However, this doesn't transfer the metadata...

> If in addition you want to keep
> the complete header information, you need to explicitly pass it to the table.meta data, i.e.
> 
> astropy.table.Table(binhdu.data, meta=binhdu.header)
> 
> so you may say this still requires a wrapper, but it?s a pretty thin one.

I agree - this is the way to go for now.  THAT thin a wrapper for a single HDU->Table conversion would be elegant but is otherwise unnecessary.  However,  mutiple table in a multiple HDU list require more work and it would be nice to have a wrapper for that.  It would be good to have this mentioned in the docs, something like

	----------------------------------------------------------------------------------------------------------------------------------------
	The equivalent reverse conversion for complex HDUList's (multiple tables in one FITS binary table file)

		tables = hdulist_to_tables (hdul)

	is easily achieved by explicitly passing both the data and the metadata to Table():

		import astropy.io.fits
		from astropy.table import Table

		def hdulist_to_tables (hdul) :
			tables = []
			for i in range(1,len(hdul)) :
				hdu = hdul[i]
				t = Table (data=hdu.data, meta=hdu.header)
				tables.append(t)
			return tables
	----------------------------------------------------------------------------------------------------------------------------------------

> I stand corrected here: Table.read() does store the header cards in the meta attribute,
> after stripping the functional keywords defining the table itself and a couple of other blacklisted
> cards - which just happened to be *all* of the cards in some of the test files in the distribution.
> In contrast, this works as expected:
> 
>>>> chandra = Table.read('https://github.com/astropy/astropy/blob/master/astropy/io/fits/tests/data/chandra_time.fits?raw=true?)
>>>> chandra.meta['TITLE']
>>>> Multiwavelength Characterization of Candidate Black Holes in Nearby Dwarf Galaxies

OK, so I wrote the test script

	http://www.astro.physik.uni-goettingen.de/~hessman/misc/HDUList_to_Table_test.py

which creates different multiple table HDULists from scratch, writes them to files (for a Table.read({filename}) comparison), and reads the last table into a Table using

    t = Table.read (hdul,hdu=n)

(hdul is the HDUList, n is the total number of HDU's; hdu=0 is the PrimaryHDU) and this appears to work: the correct table is converted.  However, I get 

	FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters

the first time and

	WARNING: hdu= was not specified but multiple tables are present, reading in first available table (hdu=1) [astropy.io.fits.connect]

for n > 2 (i.e. more than one table), even though "hdu=" _was_ specified and the correct HDU is converted; the "first available table" is NOT read.    A small bug in the irrelevant warning.

Thus, for now

	----------------------------------------------------------------------------------------------------------------------------------------
	or by using the hdu= argument of Table.read():

		def hdulist_to_tables (hdul) :
			tables = []
			for i in range(1,len(hdul)) :
				t = Table.read (hdul, hdu=i)
				tables.append(t)
			return tables

	and ignoring the warning that hdu= was not specified and that the first HDU was used (Version XXXX and earlier).		
	----------------------------------------------------------------------------------------------------------------------------------------

Rick

------------------------------------------------------------------------------------------------
Dr. Frederic V. Hessman     Hessman at Astro.physik.Uni-Goettingen.DE
Institut f?r Astrophysik          Tel.  +49-551-39-5052
Friedrich-Hund-Platz 1         Fax +49-551-39-5043
37077 Goettingen                 Room F04-133
http://www.Astro.physik.Uni-Goettingen.de/~hessman
-------------------------------------------------------------------------------------------------
MONET: a MOnitoring NEtwork of Telescopes
http://monet.Uni-Goettingen.de
-------------------------------------------------------------------------------------------------



From derek at astro.physik.uni-goettingen.de  Thu Apr 18 08:35:11 2019
From: derek at astro.physik.uni-goettingen.de (Derek Homeier)
Date: Thu, 18 Apr 2019 14:35:11 +0200
Subject: [AstroPy] AstroPy Digest: HDU to Table
In-Reply-To: <A9F5C910-FB8C-4477-909F-AEBD28AD8EBC@astro.physik.uni-goettingen.de>
References: <mailman.3356.1555540862.2981.astropy@python.org>
 <A9F5C910-FB8C-4477-909F-AEBD28AD8EBC@astro.physik.uni-goettingen.de>
Message-ID: <F28B2316-2B3D-46B0-A2CB-463EA1255978@astro.physik.uni-goettingen.de>

Hi Rick,
> 
> I agree - this is the way to go for now.  THAT thin a wrapper for a single HDU->Table conversion would be elegant but is otherwise unnecessary.  However,  mutiple table in a multiple HDU list require more work and it would be nice to have a wrapper for that.  It would be good to have this mentioned in the docs, something like
> 
> 	----------------------------------------------------------------------------------------------------------------------------------------
> 	The equivalent reverse conversion for complex HDUList's (multiple tables in one FITS binary table file)
> 
> 		tables = hdulist_to_tables (hdul)
> 
> 	is easily achieved by explicitly passing both the data and the metadata to Table():
> 
for the docs it would probably be best to recommend the ?trick? using Table.read() below.
> 
> OK, so I wrote the test script
> 
> 	http://www.astro.physik.uni-goettingen.de/~hessman/misc/HDUList_to_Table_test.py
> 
> which creates different multiple table HDULists from scratch, writes them to files (for a Table.read({filename}) comparison), and reads the last table into a Table using
> 
>    t = Table.read (hdul,hdu=n)
> 
> (hdul is the HDUList, n is the total number of HDU's; hdu=0 is the PrimaryHDU) and this appears to work: the correct table is converted.  However, I get 
> 
> 	FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
>  from ._conv import register_converters as _register_converters
> 
> the first time and
> 
Hmm,  don?t see that FutureWarning with Astropy 3.1.2 + Numpy 1.14.5 - in fact I could not find that
code line anywhere in the astropy or numpy tree.

> 	WARNING: hdu= was not specified but multiple tables are present, reading in first available table (hdu=1) [astropy.io.fits.connect]
> 
> for n > 2 (i.e. more than one table), even though "hdu=" _was_ specified and the correct HDU is converted; the "first available table" is NOT read.    A small bug in the irrelevant warning.
> 
But the ?hdu= was not specified? warning (correctly) follows the reading from file, and that is is opening the
first extension - looks all correct to me. I tested with all extensions in hdul (extending your last lines a bit):
...
	t = Table.read ('test.fits',format='fits')
	t.info
	print ('  * y-sum of table:',np.sum(t['y']))

	print (' * Creating a table from default (first) table in HDUList ?')
	t = Table.read (hdul)
	t.info
	print ('  * y-sum of table:',np.sum(t['y']))

	print ('  * Creating a table from the each table in HDUList using hdu= argument ...')
	for i in range(1, n+1) :
		t = Table.read (hdul,hdu=i)
		t.info
		print ('  * HDU {:d} - {:s}: y-sum of table: {:f}'.format(i, t.meta['OBJNAME'], np.sum(t['y'])))

?
  * Creating a table from the file...
WARNING: hdu= was not specified but multiple tables are present, reading in first available table (hdu=1) [astropy.io.fits.connect]
  * y-sum of table: 55.0
  * Creating a table from default (first) table in HDUList ...
  * y-sum of table: 55.0
  * Creating a table from the each table in HDUList using hdu= argument ...
  * HDU 1 - data_0: y-sum of table: 55.000000
  * HDU 2 - data_1: y-sum of table: 550.000000

* Test using 3 HDUs...
  * y-sum of table: 55.0
  * y-sum of table: 550.0
  * y-sum of table: 5500.0
  * Storing in file...
  * Creating a table from the file...
  * y-sum of table: 55.0
  * Creating a table from default (first) table in HDUList ...
  * y-sum of table: 55.0
  * Creating a table from the each table in HDUList using hdu= argument ...
  * HDU 1 - data_0: y-sum of table: 55.000000
  * HDU 2 - data_1: y-sum of table: 550.000000
  * HDU 3 - data_2: y-sum of table: 5500.000000

Creating lists of table is thus straightforward; and as `table_to_hdu()` does not provide any more
specific functionality here either, I rather don?t think it needs to be further discussed in the docs.
At a minimum probably a paragraph should be added to the end of the `Reading` section noting
that in addition to the file-like objects mentioned in http://docs.astropy.org/en/stable/io/unified.html
Table.read() accepts an HDU or HDUList object as input ?file? (with the ?hdu=? kwarg functioning
accordingly in the latter case).

Cheers,
					Derek


From algorithm059 at gmail.com  Thu Apr  4 04:41:24 2019
From: algorithm059 at gmail.com (Rohit Kapoor)
Date: Thu, 04 Apr 2019 08:41:24 -0000
Subject: [AstroPy] Introduction and query regarding installation
Message-ID: <CAECg8aNP0LKL_B+L3QD10NjP=CM_CRRx5o51bedECc5KN9oAuw@mail.gmail.com>

Hello all!
I am using Anaconda distribution and have created a virtual environment
named space. I just installed astropy in that environment and configured
it's developer version as per the instructions given here
<http://docs.astropy.org/en/stable/development/workflow/get_devel_version.html#get-devel>
. When I run the conda list command on the terminal i get the output as
shown in the image.

I installed astropy's developer version using pip in the conda environment
where astropy was already installed using conda. Also i ran the command:
"python setup.py test" and it gave me a positive result and no errors. So i
just want to confirm if the installation is complete.


Thank you
-Rohit
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