From npross at roe.ac.uk  Mon Sep  2 08:53:54 2019
From: npross at roe.ac.uk (Nicholas Ross)
Date: Mon, 2 Sep 2019 12:53:54 +0000
Subject: [AstroPy] SpecViz and SpecUtils
In-Reply-To: <mailman.29.1567008003.30099.astropy@python.org>
References: <mailman.29.1567008003.30099.astropy@python.org>
Message-ID: <6607D51E-7D4F-4F81-825F-11EDAAEE2B27@roe.ac.uk>

Dear All, 

I?m keen to starting using SpecViz and SpecUtils in my research analyses. 
I?ve followed the instructions at
	https://specviz.readthedocs.io/en/stable/installation.html

but when I come to run specviz on the command line, I get::

> specviz
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/3.7/bin/specviz", line 11, in <module>
    load_entry_point('specviz==0.3.0', 'console_scripts', 'specviz')()
  File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pkg_resources/__init__.py", line 489, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2793, in load_entry_point
    return ep.load()
  File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2411, in load
    return self.resolve()
  File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2417, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/specviz-0.3.0-py3.7.egg/specviz/__init__.py", line 17, in <module>
    from . import analysis
  File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/specviz-0.3.0-py3.7.egg/specviz/analysis/__init__.py", line 3, in <module>
    from .statistics import *
  File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/specviz-0.3.0-py3.7.egg/specviz/analysis/statistics.py", line 10, in <module>
    from ..core.data import Spectrum1DRef
  File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/specviz-0.3.0-py3.7.egg/specviz/core/data.py", line 15, in <module>
    from specutils.core.generic import Spectrum1DRef
ModuleNotFoundError: No module named ?specutils.core'

However(!!) if I then do: 
	> ipython 
	In [1]: import specutils.core as core                                                                                                                                                                                                                
	WARNING: AstropyDeprecationWarning: astropy.extern.six will be removed in 4.0, use the six module directly if it is still needed [astropy.extern.six]
	In [2]: from specutils.core.generic import Spectrum1DRef                                                                                                                                                                                            
	In [3]:  


? it definitely seems as if I have specutils installed. 

Do we know what might be going on here??!!

Many thanks as usual, 
Nic


====================================
  Dr. Nicholas P. Ross
  STFC Ernest Rutherford Fellow
  Institute for Astronomy
  University of Edinburgh
  Royal Observatory, Blackford Hill 
  Edinburgh EH9 3HJ, United Kingdom
  +44 (0)131-668 8351
  d80b2t.github.io
====================================




From contact at nicholasearl.me  Tue Sep  3 13:12:09 2019
From: contact at nicholasearl.me (Nicholas Earl)
Date: Tue, 03 Sep 2019 13:12:09 -0400
Subject: [AstroPy] SpecViz and SpecUtils
In-Reply-To: <6607D51E-7D4F-4F81-825F-11EDAAEE2B27@roe.ac.uk>
References: <mailman.29.1567008003.30099.astropy@python.org>
 <6607D51E-7D4F-4F81-825F-11EDAAEE2B27@roe.ac.uk>
Message-ID: <5100fc30-031a-4ee4-8d98-f4fe87a7631f@www.fastmail.com>

Hi Nic,

Specutils hasn't had a 'core' module in several versions, and it looks like you're attempting to install SpecViz v0.3.0 (where as the current version is 0.7.0). How are you attempting to install SpecViz (through anaconda, pip, or from source)?

Cheers,
Nick

On Mon, Sep 2, 2019, at 8:53 AM, Nicholas Ross wrote:
> Dear All, 
> 
> I?m keen to starting using SpecViz and SpecUtils in my research analyses. 
> I?ve followed the instructions at
> 	https://specviz.readthedocs.io/en/stable/installation.html
> 
> but when I come to run specviz on the command line, I get::
> 
> > specviz
> Traceback (most recent call last):
>   File "/Library/Frameworks/Python.framework/Versions/3.7/bin/specviz", 
> line 11, in <module>
>     load_entry_point('specviz==0.3.0', 'console_scripts', 'specviz')()
>   File 
> "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pkg_resources/__init__.py", line 489, in load_entry_point
>     return get_distribution(dist).load_entry_point(group, name)
>   File 
> "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2793, in load_entry_point
>     return ep.load()
>   File 
> "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2411, in load
>     return self.resolve()
>   File 
> "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2417, in resolve
>     module = __import__(self.module_name, fromlist=['__name__'], 
> level=0)
>   File 
> "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/specviz-0.3.0-py3.7.egg/specviz/__init__.py", line 17, in <module>
>     from . import analysis
>   File 
> "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/specviz-0.3.0-py3.7.egg/specviz/analysis/__init__.py", line 3, in <module>
>     from .statistics import *
>   File 
> "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/specviz-0.3.0-py3.7.egg/specviz/analysis/statistics.py", line 10, in <module>
>     from ..core.data import Spectrum1DRef
>   File 
> "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/specviz-0.3.0-py3.7.egg/specviz/core/data.py", line 15, in <module>
>     from specutils.core.generic import Spectrum1DRef
> ModuleNotFoundError: No module named ?specutils.core'
> 
> However(!!) if I then do: 
> 	> ipython 
> 	In [1]: import specutils.core as core                                  
>                                                                         
>                                                                         
>                               
> 	WARNING: AstropyDeprecationWarning: astropy.extern.six will be removed 
> in 4.0, use the six module directly if it is still needed 
> [astropy.extern.six]
> 	In [2]: from specutils.core.generic import Spectrum1DRef               
>                                                                         
>                                                                         
>                              
> 	In [3]:  
> 
> 
> ? it definitely seems as if I have specutils installed. 
> 
> Do we know what might be going on here??!!
> 
> Many thanks as usual, 
> Nic
> 
> 
> ====================================
>   Dr. Nicholas P. Ross
>   STFC Ernest Rutherford Fellow
>   Institute for Astronomy
>   University of Edinburgh
>   Royal Observatory, Blackford Hill 
>   Edinburgh EH9 3HJ, United Kingdom
>   +44 (0)131-668 8351
>   d80b2t.github.io
> ====================================
> 
> 
> 
> _______________________________________________
> AstroPy mailing list
> AstroPy at python.org
> https://mail.python.org/mailman/listinfo/astropy
>

From keith at sloan-home.co.uk  Sun Sep  8 10:43:55 2019
From: keith at sloan-home.co.uk (keith)
Date: Sun, 8 Sep 2019 15:43:55 +0100
Subject: [AstroPy] Storing results into Tables for further SQL queries.
Message-ID: <54d772e2-7971-9437-029a-2c48a0eb2afc@sloan-home.co.uk>

Apologies for a newby question.

For my MSc project I need? to run SQL queries against GAMA and SDSS.

I am using Jupyter on Ubuntu 18.04.

I can successfully retrieve data by using the astropy python modules.

I would like to store the results from the more complicated SQL queries 
into a Table,
so that I can perform further joins on both GAMA and SDSS? tables.

How do I go about this?

Do I have to setup a local database?

Thanks

-- 
========== Art & Ceramics ===========
https://www.instagram.com/ksloan1952/


From trive at astro.su.se  Mon Sep  9 05:20:28 2019
From: trive at astro.su.se (T. Emil Rivera-Thorsen)
Date: Mon, 9 Sep 2019 11:20:28 +0200
Subject: [AstroPy] Storing results into Tables for further SQL queries.
In-Reply-To: <54d772e2-7971-9437-029a-2c48a0eb2afc@sloan-home.co.uk>
References: <54d772e2-7971-9437-029a-2c48a0eb2afc@sloan-home.co.uk>
Message-ID: <775b0ee5-4d3c-4941-16cf-57324f16256e@astro.su.se>

Hi Keith.

I don?t know the specifics of your project in detail, but is sounds like 
a job for the Pandas module, which is good at labeled, heterogeneous 
data and light database-like operations like joine, merge, pivot etc.

http://pandas.pydata.org

/Emil


On 9/8/19 4:43 PM, keith wrote:
> Apologies for a newby question.
>
> For my MSc project I need? to run SQL queries against GAMA and SDSS.
>
> I am using Jupyter on Ubuntu 18.04.
>
> I can successfully retrieve data by using the astropy python modules.
>
> I would like to store the results from the more complicated SQL queries
> into a Table,
> so that I can perform further joins on both GAMA and SDSS tables.
>
> How do I go about this?
>
> Do I have to setup a local database?
>
> Thanks
>
> -- 
> ========== Art & Ceramics ===========
> https://www.instagram.com/ksloan1952/
>
> _______________________________________________
> AstroPy mailing list
> AstroPy at python.org
> https://mail.python.org/mailman/listinfo/astropy
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From mcraig at mnstate.edu  Mon Sep  9 10:34:50 2019
From: mcraig at mnstate.edu (Craig, Matthew W)
Date: Mon, 9 Sep 2019 14:34:50 +0000
Subject: [AstroPy] ccdproc 2!
Message-ID: <ED94B36E-8BD9-4D2D-9EEC-CE7D9DCBBABB@minnstate.edu>

Hi,

We are delighted to announce the release of ccdproc version 2.  See ccdproc.readthedocs.io for installation instructions or read on...

This is the first release of ccdproc that is Python 3 only!

A special thanks to first-time code contributors Jaime A. Alvarado-Montes, Julio C. N. Campagnolo, Mihai Cara, Michael Hlabathe, and Luca Rizzi, and to everyone who opened issues.

**New and improved**

The `ImageFileCollection` for working with sets of images has several new features:

	+ Construct a collection from an explicit list of files.
	+ Filter files using regular expression matching.
	+ Create a new collection by filtering an existing collection.

**Other new features include:**

	+ Weights in image combination can be a 1D array.
	+ Reduced memory in image combination.
	+ Many fewer files open during image combination when using memory mapping and breaking the image stack into chunks.
	+ Better performance and a wider array of compression types for `ImageFileCollection`.
	+ Better handling of constructing error array when some image value are negative.
	+ Better computation of boolean mask from bit planes.

?> In addition, several bugs were fixed: https://github.com/astropy/ccdproc/blob/v2.0.0/CHANGES.rst


**Installation**

You can install the latest version (which is actually 2.0.1) with conda or with pip:

conda install -c astropy ccdproc=2

OR

pip install ccdproc

If you are updating from an earlier version of ccdproc using pip do this: pip install -U ccdproc

Sincerely,

Matt Craig, Steve Crawford and Michael Seifert
ccdproc maintainers


From martinberoiz at gmail.com  Mon Sep  9 11:20:05 2019
From: martinberoiz at gmail.com (Martin Beroiz)
Date: Mon, 9 Sep 2019 10:20:05 -0500
Subject: [AstroPy] question about RotateNative2Celestial
In-Reply-To: <a489a51a-02cf-4ec1-808e-d580306734e5@Spark>
References: <a489a51a-02cf-4ec1-808e-d580306734e5@Spark>
Message-ID: <1346a89d-3f77-4242-a39e-a071f7524cb7@Spark>

Hello,

I?m toying a little with WCS and?the functions on astropy.modeling.rotations.
I?m not sure if I found a bug or if I don?t understand yet the API for?RotateNative2Celestial
Here?s the small example that I came up with and the traceback I get

from astropy.modeling import rotations as r
lon = 100.00
lat = -63.00
alpha_c = 100.00
delta_c = -63.00
lon_pole = 180.0

n2c = r.RotateNative2Celestial(lon, lat, lon_pole)
n2c.evaluate(0., 90., lon, lat, lon_pole)

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-4-0a1e86053054> in <module>
----> 1 n2c.evaluate(0., 90., lon, lat, lon_pole)

~/anaconda3/lib/python3.7/site-packages/astropy/modeling/rotations.py in evaluate(self, phi_N, theta_N, lon, lat, lon_pole)
   252         theta = - (np.pi / 2 - lat)
   253         psi = -(np.pi / 2 + lon)
--> 254         alpha_C, delta_C = super()._evaluate(phi_N, theta_N, phi, theta, psi)
   255         return alpha_C, delta_C
   256

~/anaconda3/lib/python3.7/site-packages/astropy/modeling/rotations.py in _evaluate(self, phi, theta, lon, lat, lon_pole)
   183     def _evaluate(self, phi, theta, lon, lat, lon_pole):
   184         alpha, delta = super().evaluate(phi, theta, lon, lat, lon_pole,
--> 185                                         self.axes_order)
   186         mask = alpha < 0
   187         if isinstance(mask, np.ndarray):

~/anaconda3/lib/python3.7/site-packages/astropy/modeling/rotations.py in evaluate(self, alpha, delta, phi, theta, psi, axes_order)
    89             shape = alpha.shape
    90         inp = self.spherical2cartesian(alpha, delta)
---> 91         matrix = self._create_matrix(phi, theta, psi, axes_order)
    92         result = np.dot(matrix, inp)
    93         a, b = self.cartesian2spherical(*result)

~/anaconda3/lib/python3.7/site-packages/astropy/modeling/rotations.py in _create_matrix(self, phi, theta, psi, axes_order)
    47             if isinstance(angle, u.Quantity):
    48                 angle = angle.value
---> 49             angle = angle.item()
    50             matrices.append(rotation_matrix(angle, axis, unit=u.rad))
    51         result = matrix_product(*matrices[::-1])

AttributeError: 'float' object has no attribute 'item'


I don't understand why it is expecting `angle` to have the `item` attribute.

Does anyone know what I'm doing wrong? Any help would be much appreciated.

Thanks!
M.




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From aldcroft at head.cfa.harvard.edu  Mon Sep  9 13:33:35 2019
From: aldcroft at head.cfa.harvard.edu (Aldcroft, Thomas)
Date: Mon, 9 Sep 2019 13:33:35 -0400
Subject: [AstroPy] Storing results into Tables for further SQL queries.
In-Reply-To: <54d772e2-7971-9437-029a-2c48a0eb2afc@sloan-home.co.uk>
References: <54d772e2-7971-9437-029a-2c48a0eb2afc@sloan-home.co.uk>
Message-ID: <CAMtEP6wCxaus5pMMF_+GHA6yAy39P-y2McLRi2_DpNV9K0bcfw@mail.gmail.com>

Hi Keith,

With the astropy Table object you can do table operations like join and
merge:

https://docs.astropy.org/en/stable/table/operations.html#table-operations

I'm not entirely clear if your question is about how to get your SQL query
results into a Table, or how to do joins with a Table.  Can you provide a
bit more detail?

- Tom

On Sun, Sep 8, 2019 at 10:44 AM keith <keith at sloan-home.co.uk> wrote:

> Apologies for a newby question.
>
> For my MSc project I need  to run SQL queries against GAMA and SDSS.
>
> I am using Jupyter on Ubuntu 18.04.
>
> I can successfully retrieve data by using the astropy python modules.
>
> I would like to store the results from the more complicated SQL queries
> into a Table,
> so that I can perform further joins on both GAMA and SDSS  tables.
>
> How do I go about this?
>
> Do I have to setup a local database?
>
> Thanks
>
> --
> ========== Art & Ceramics ===========
> https://www.instagram.com/ksloan1952/
>
> _______________________________________________
> AstroPy mailing list
> AstroPy at python.org
> https://mail.python.org/mailman/listinfo/astropy
>
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From keith at sloan-home.co.uk  Mon Sep  9 13:44:16 2019
From: keith at sloan-home.co.uk (keith)
Date: Mon, 9 Sep 2019 18:44:16 +0100
Subject: [AstroPy] Storing results into Tables for further SQL queries.
In-Reply-To: <CAMtEP6wCxaus5pMMF_+GHA6yAy39P-y2McLRi2_DpNV9K0bcfw@mail.gmail.com>
References: <54d772e2-7971-9437-029a-2c48a0eb2afc@sloan-home.co.uk>
 <CAMtEP6wCxaus5pMMF_+GHA6yAy39P-y2McLRi2_DpNV9K0bcfw@mail.gmail.com>
Message-ID: <aa9db3a6-1c33-7b19-aa10-2e9e1f3c29d1@sloan-home.co.uk>

Below is the sort of thing I would like to do from python for both GAMA 
and SDSS

It is an example of my use of the SDSS CasJob facility I would like to 
do the same from python and similar accessing GAMA. The way the CasJob 
seems to work is to store to an external database as the query specifies 
into mydb.E_Galaxies where mydb is particular to my login and the other 
tables are available i.e. DR15.Galaxy

Having created mydb.E_Galaxies I would then use the table in future 
joins etc without having to repeat the execution for a large number of 
future queries.

SELECT TOP 5000 ObjID,r,g,i,u,u-r as redness into mydb.E_Galaxies from 
DR15.Galaxy as G
WHERE
G.lnlDev_r > G.lnlExp_r + 0.1
and G.lnlExp_r > -999

and (G.flags & (dbo.fPhotoFlags('BINNED1') + dbo.fPhotoFlags('BINNED2') 
+ dbo.fPhotoFlags('BINNED4'))) > 0

and (G.flags & ( dbo.fPhotoFlags('BLENDED') + 
dbo.fPhotoFlags('NODEBLEND') + dbo.fPhotoFlags('CHILD'))) != 
dbo.fPhotoFlags('BLENDED')

and (G.flags & (dbo.fPhotoFlags('EDGE') + dbo.fPhotoFlags('SATURATED'))) = 0

and G.petroMag_i > 17.5

and (G.petroMag_r > 15.5 or G.petror50_r > 2)
and (G.petroMag_r > 0 and G.g > 0 and G.r > 0 and G.i > 0)
and ( (G.petroMag_r - G.extinction_r) < 19.2
and (G.petroMag_r - G.extinction_r <
(13.1 + (7/3)*(G.g - G.r) + 4 *(G.r - G.i) - 4 * 0.18 ) )
and ( (G.r - G.i - (G.g - G.r)/4 - 0.18) < 0.2 )
and ( (G.r - G.i - (G.g - G.r)/4 - 0.18) > -0.2 ) )
or ( (G.petroMag_r - G.extinction_r < 19.5)
and ( (G.r - G.i - (G.g - G.r)/4 - 0.18) >
(0.45 - 4*(G.g - G.r) ) )
and ( (G.g - G.r) > (1.35 + 0.25 *(G.r - G.i) ) ) )

On 09/09/2019 18:33, Aldcroft, Thomas wrote:
> Hi Keith,
>
> With the astropy Table object you can do table operations like join 
> and merge:
>
> https://docs.astropy.org/en/stable/table/operations.html#table-operations
>
> I'm not entirely clear if your question is about how to get your SQL 
> query results into a Table, or how to do joins with a Table.? Can you 
> provide a bit more detail?
>
> - Tom
>
> On Sun, Sep 8, 2019 at 10:44 AM keith <keith at sloan-home.co.uk 
> <mailto:keith at sloan-home.co.uk>> wrote:
>
>     Apologies for a newby question.
>
>     For my MSc project I need? to run SQL queries against GAMA and SDSS.
>
>     I am using Jupyter on Ubuntu 18.04.
>
>     I can successfully retrieve data by using the astropy python modules.
>
>     I would like to store the results from the more complicated SQL
>     queries
>     into a Table,
>     so that I can perform further joins on both GAMA and SDSS tables.
>
>     How do I go about this?
>
>     Do I have to setup a local database?
>
>     Thanks
>
>     -- 
>     ========== Art & Ceramics ===========
>     https://www.instagram.com/ksloan1952/
>
>     _______________________________________________
>     AstroPy mailing list
>     AstroPy at python.org <mailto: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

-- 
========== Art & Ceramics ===========
https://www.instagram.com/ksloan1952/

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From stefano.covino at gmail.com  Mon Sep  9 13:51:17 2019
From: stefano.covino at gmail.com (Covino, Stefano)
Date: Mon, 9 Sep 2019 19:51:17 +0200
Subject: [AstroPy] Storing results into Tables for further SQL queries.
In-Reply-To: <aa9db3a6-1c33-7b19-aa10-2e9e1f3c29d1@sloan-home.co.uk>
References: <54d772e2-7971-9437-029a-2c48a0eb2afc@sloan-home.co.uk>
 <CAMtEP6wCxaus5pMMF_+GHA6yAy39P-y2McLRi2_DpNV9K0bcfw@mail.gmail.com>
 <aa9db3a6-1c33-7b19-aa10-2e9e1f3c29d1@sloan-home.co.uk>
Message-ID: <CAMYLZN-WxfQzaS2dYPqYRfC6memPuiQuxpY1kA1P5nvS3qgNUw@mail.gmail.com>

Probably something like this could work:?

import mysql.connector as pm
from astropy.table import Table


def readMySQLTable (ihost, idbase, iuser, ipwd, icmd):
    db = pm.connect(user=iuser, password=ipwd, host=ihost, database=idbase,
connect_timeout=60)
    cursor = db.cursor()
    cursor.execute(icmd)
    cols = cursor.column_names
    dt = [a for a in cursor]
    t = Table(rows=dt,names=cols)
    return t

Where ?icmd? is the sql command.

   Stefano



Il giorno luned? 9 settembre 2019, keith <keith at sloan-home.co.uk> ha
scritto:

> Below is the sort of thing I would like to do from python for both GAMA
> and SDSS
>
> It is an example of my use of the SDSS CasJob facility I would like to do
> the same from python and similar accessing GAMA. The way the CasJob seems
> to work is to store to an external database as the query specifies into mydb.E_Galaxies
> where mydb is particular to my login and the other tables are available
> i.e. DR15.Galaxy
>
> Having created mydb.E_Galaxies I would then use the table in future joins
> etc without having to repeat the execution for a large number of future
> queries.
>
> SELECT TOP 5000 ObjID,r,g,i,u,u-r as redness into mydb.E_Galaxies from
> DR15.Galaxy as G
> WHERE
> G.lnlDev_r > G.lnlExp_r + 0.1
> and G.lnlExp_r > -999
>
> and (G.flags & (dbo.fPhotoFlags('BINNED1') + dbo.fPhotoFlags('BINNED2') +
> dbo.fPhotoFlags('BINNED4'))) > 0
>
> and (G.flags & ( dbo.fPhotoFlags('BLENDED') + dbo.fPhotoFlags('NODEBLEND')
> + dbo.fPhotoFlags('CHILD'))) != dbo.fPhotoFlags('BLENDED')
>
> and (G.flags & (dbo.fPhotoFlags('EDGE') + dbo.fPhotoFlags('SATURATED'))) =
> 0
>
> and G.petroMag_i > 17.5
>
> and (G.petroMag_r > 15.5 or G.petror50_r > 2)
> and (G.petroMag_r > 0 and G.g > 0 and G.r > 0 and G.i > 0)
> and ( (G.petroMag_r - G.extinction_r) < 19.2
> and (G.petroMag_r - G.extinction_r <
> (13.1 + (7/3)*(G.g - G.r) + 4 *(G.r - G.i) - 4 * 0.18 ) )
> and ( (G.r - G.i - (G.g - G.r)/4 - 0.18) < 0.2 )
> and ( (G.r - G.i - (G.g - G.r)/4 - 0.18) > -0.2 ) )
> or ( (G.petroMag_r - G.extinction_r < 19.5)
> and ( (G.r - G.i - (G.g - G.r)/4 - 0.18) >
> (0.45 - 4*(G.g - G.r) ) )
> and ( (G.g - G.r) > (1.35 + 0.25 *(G.r - G.i) ) ) )
> On 09/09/2019 18:33, Aldcroft, Thomas wrote:
>
> Hi Keith,
>
> With the astropy Table object you can do table operations like join and
> merge:
>
> https://docs.astropy.org/en/stable/table/operations.html#table-operations
>
> I'm not entirely clear if your question is about how to get your SQL query
> results into a Table, or how to do joins with a Table.  Can you provide a
> bit more detail?
>
> - Tom
>
> On Sun, Sep 8, 2019 at 10:44 AM keith <keith at sloan-home.co.uk> wrote:
>
>> Apologies for a newby question.
>>
>> For my MSc project I need  to run SQL queries against GAMA and SDSS.
>>
>> I am using Jupyter on Ubuntu 18.04.
>>
>> I can successfully retrieve data by using the astropy python modules.
>>
>> I would like to store the results from the more complicated SQL queries
>> into a Table,
>> so that I can perform further joins on both GAMA and SDSS  tables.
>>
>> How do I go about this?
>>
>> Do I have to setup a local database?
>>
>> Thanks
>>
>> --
>> ========== Art & Ceramics ===========
>> https://www.instagram.com/ksloan1952/
>>
>> _______________________________________________
>> AstroPy mailing list
>> AstroPy at python.org
>> https://mail.python.org/mailman/listinfo/astropy
>>
>
> _______________________________________________
> AstroPy mailing listAstroPy at python.orghttps://mail.python.org/mailman/listinfo/astropy
>
> --
> ========== Art & Ceramics ===========https://www.instagram.com/ksloan1952/
>
>
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From keith at sloan-home.co.uk  Mon Sep  9 14:12:19 2019
From: keith at sloan-home.co.uk (keith)
Date: Mon, 9 Sep 2019 19:12:19 +0100
Subject: [AstroPy] I think I made a mix up of names ( Trouble being Similar )
In-Reply-To: <CAMYLZN-WxfQzaS2dYPqYRfC6memPuiQuxpY1kA1P5nvS3qgNUw@mail.gmail.com>
References: <54d772e2-7971-9437-029a-2c48a0eb2afc@sloan-home.co.uk>
 <CAMtEP6wCxaus5pMMF_+GHA6yAy39P-y2McLRi2_DpNV9K0bcfw@mail.gmail.com>
 <aa9db3a6-1c33-7b19-aa10-2e9e1f3c29d1@sloan-home.co.uk>
 <CAMYLZN-WxfQzaS2dYPqYRfC6memPuiQuxpY1kA1P5nvS3qgNUw@mail.gmail.com>
Message-ID: <b77b49e6-f0c3-af35-3edf-6e5349f646c9@sloan-home.co.uk>

I would like to store results from astroquery requests for subsequent 
astroquery requests.

i.e. make query with

from astroquery.gama import GAMA
result = GAMA.query_sql('SELECT * FROM SpecAll LIMIT 100')

and

from astroquery.sdss import SDSS
result = SDSS.query_sql('SELECT * FROM SpecAll LIMIT 100')

i.e. https://astroquery.readthedocs.io/en/latest/index.html#

Or is that a different mailing list




On 09/09/2019 18:51, Covino, Stefano wrote:
> Probably something like this could work:?
>
> import mysql.connector as pm
> from astropy.table import Table
>
>
> def readMySQLTable (ihost, idbase, iuser, ipwd, icmd):
> ? ? db = pm.connect(user=iuser, password=ipwd, host=ihost, 
> database=idbase, connect_timeout=60)
> ? ? cursor = db.cursor()
> ? ? cursor.execute(icmd)
> ? ? cols = cursor.column_names
> ? ? dt = [a for a in cursor]
> ? ? t = Table(rows=dt,names=cols)
> ? ? return t
>
> Where ?icmd? is the sql command.
>
> ? ?Stefano
>
>
>
> Il giorno luned? 9 settembre 2019, keith <keith at sloan-home.co.uk 
> <mailto:keith at sloan-home.co.uk>> ha scritto:
>
>     Below is the sort of thing I would like to do from python for both
>     GAMA and SDSS
>
>     It is an example of my use of the SDSS CasJob facility I would
>     like to do the same from python and similar accessing GAMA. The
>     way the CasJob seems to work is to store to an external database
>     as the query specifies into mydb.E_Galaxies where mydb is
>     particular to my login and the other tables are available i.e.
>     DR15.Galaxy
>
>     Having created mydb.E_Galaxies I would then use the table in
>     future joins etc without having to repeat the execution for a
>     large number of future queries.
>
>     SELECT TOP 5000 ObjID,r,g,i,u,u-r as redness into mydb.E_Galaxies
>     from DR15.Galaxy as G
>     WHERE
>     G.lnlDev_r > G.lnlExp_r + 0.1
>     and G.lnlExp_r > -999
>
>     and (G.flags & (dbo.fPhotoFlags('BINNED1') +
>     dbo.fPhotoFlags('BINNED2') + dbo.fPhotoFlags('BINNED4'))) > 0
>
>     and (G.flags & ( dbo.fPhotoFlags('BLENDED') +
>     dbo.fPhotoFlags('NODEBLEND') + dbo.fPhotoFlags('CHILD'))) !=
>     dbo.fPhotoFlags('BLENDED')
>
>     and (G.flags & (dbo.fPhotoFlags('EDGE') +
>     dbo.fPhotoFlags('SATURATED'))) = 0
>
>     and G.petroMag_i > 17.5
>
>     and (G.petroMag_r > 15.5 or G.petror50_r > 2)
>     and (G.petroMag_r > 0 and G.g > 0 and G.r > 0 and G.i > 0)
>     and ( (G.petroMag_r - G.extinction_r) < 19.2
>     and (G.petroMag_r - G.extinction_r <
>     (13.1 + (7/3)*(G.g - G.r) + 4 *(G.r - G.i) - 4 * 0.18 ) )
>     and ( (G.r - G.i - (G.g - G.r)/4 - 0.18) < 0.2 )
>     and ( (G.r - G.i - (G.g - G.r)/4 - 0.18) > -0.2 ) )
>     or ( (G.petroMag_r - G.extinction_r < 19.5)
>     and ( (G.r - G.i - (G.g - G.r)/4 - 0.18) >
>     (0.45 - 4*(G.g - G.r) ) )
>     and ( (G.g - G.r) > (1.35 + 0.25 *(G.r - G.i) ) ) )
>
>     On 09/09/2019 18:33, Aldcroft, Thomas wrote:
>>     Hi Keith,
>>
>>     With the astropy Table object you can do table operations like
>>     join and merge:
>>
>>     https://docs.astropy.org/en/stable/table/operations.html#table-operations
>>     <https://docs.astropy.org/en/stable/table/operations.html#table-operations>
>>
>>     I'm not entirely clear if your question is about how to get your
>>     SQL query results into a Table, or how to do joins with a Table.?
>>     Can you provide a bit more detail?
>>
>>     - Tom
>>
>>     On Sun, Sep 8, 2019 at 10:44 AM keith <keith at sloan-home.co.uk
>>     <mailto:keith at sloan-home.co.uk>> wrote:
>>
>>         Apologies for a newby question.
>>
>>         For my MSc project I need? to run SQL queries against GAMA
>>         and SDSS.
>>
>>         I am using Jupyter on Ubuntu 18.04.
>>
>>         I can successfully retrieve data by using the astropy python
>>         modules.
>>
>>         I would like to store the results from the more complicated
>>         SQL queries
>>         into a Table,
>>         so that I can perform further joins on both GAMA and SDSS?
>>         tables.
>>
>>         How do I go about this?
>>
>>         Do I have to setup a local database?
>>
>>         Thanks
>>
>>         -- 
>>         ========== Art & Ceramics ===========
>>         https://www.instagram.com/ksloan1952/
>>         <https://www.instagram.com/ksloan1952/>
>>
>>         _______________________________________________
>>         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>
>>
>>
>>     _______________________________________________
>>     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>
>
>     -- 
>     ========== Art & Ceramics ===========
>     https://www.instagram.com/ksloan1952/  <https://www.instagram.com/ksloan1952/>
>
>
> _______________________________________________
> AstroPy mailing list
> AstroPy at python.org
> https://mail.python.org/mailman/listinfo/astropy

-- 
========== Art & Ceramics ===========
https://www.instagram.com/ksloan1952/

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From dull4.ja at gmail.com  Mon Sep  9 18:47:18 2019
From: dull4.ja at gmail.com (James Dull)
Date: Mon, 9 Sep 2019 16:47:18 -0600
Subject: [AstroPy] Executable Script fitsheader
Message-ID: <CALykZjy7ScXQrTTeowjn3QvQC=o2HEcPjUJgHSYbdtc6LM5CPg@mail.gmail.com>

I would like to extract header information from several hundred fits files
and put it into a csv file. I ran across the executable script information
fitsheader that appears to do just that. It works perfectly for a single
file. However, when I follow the online command for that uses a wildcard so
multiple files can be completed in a single pass I get "unrecognized
command"

Something similar happens with the other scripts if I use a wildcard.

I feel I'm missing something simple.

The command I'm using is: fitsheader --table ascii.csv *.fits > keywords.csv

thanks
Jim
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From dencheva at stsci.edu  Tue Sep 10 07:25:16 2019
From: dencheva at stsci.edu (Nadia Dencheva)
Date: Tue, 10 Sep 2019 11:25:16 +0000
Subject: [AstroPy] question about RotateNative2Celestial
In-Reply-To: <1346a89d-3f77-4242-a39e-a071f7524cb7@Spark>
References: <a489a51a-02cf-4ec1-808e-d580306734e5@Spark>
 <1346a89d-3f77-4242-a39e-a071f7524cb7@Spark>
Message-ID: <625553F3-78F7-40F2-AA2C-931ECB9FC5A0@stsci.edu>

Hi Martin,

Astropy.modeling models have a ?__call__ method and are supposed to be called as functions.
The ?__call__? method does some additional reformatting of inputs and outputs (basically using
arrays internally).

Try calling it like this:

n2c(x, y)

Cheers,
Nadia

From: AstroPy <astropy-bounces+dencheva=stsci.edu at python.org> on behalf of Martin Beroiz <martinberoiz at gmail.com>
Reply-To: Astronomical Python mailing list <astropy at python.org>
Date: Monday, September 9, 2019 at 11:20 AM
To: "astropy at python.org" <astropy at python.org>
Subject: [AstroPy] question about RotateNative2Celestial

Hello,

I?m toying a little with WCS and the functions on astropy.modeling.rotations.
I?m not sure if I found a bug or if I don?t understand yet the API for RotateNative2Celestial
Here?s the small example that I came up with and the traceback I get

from astropy.modeling import rotations as r
lon = 100.00
lat = -63.00
alpha_c = 100.00
delta_c = -63.00
lon_pole = 180.0

n2c = r.RotateNative2Celestial(lon, lat, lon_pole)
n2c.evaluate(0., 90., lon, lat, lon_pole)


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

AttributeError                            Traceback (most recent call last)

<ipython-input-4-0a1e86053054> in <module>

----> 1 n2c.evaluate(0., 90., lon, lat, lon_pole)



~/anaconda3/lib/python3.7/site-packages/astropy/modeling/rotations.py in evaluate(self, phi_N, theta_N, lon, lat, lon_pole)

    252         theta = - (np.pi / 2 - lat)

    253         psi = -(np.pi / 2 + lon)

--> 254         alpha_C, delta_C = super()._evaluate(phi_N, theta_N, phi, theta, psi)

    255         return alpha_C, delta_C

    256



~/anaconda3/lib/python3.7/site-packages/astropy/modeling/rotations.py in _evaluate(self, phi, theta, lon, lat, lon_pole)

    183     def _evaluate(self, phi, theta, lon, lat, lon_pole):

    184         alpha, delta = super().evaluate(phi, theta, lon, lat, lon_pole,

--> 185                                         self.axes_order)

    186         mask = alpha < 0

    187         if isinstance(mask, np.ndarray):



~/anaconda3/lib/python3.7/site-packages/astropy/modeling/rotations.py in evaluate(self, alpha, delta, phi, theta, psi, axes_order)

     89             shape = alpha.shape

     90         inp = self.spherical2cartesian(alpha, delta)

---> 91         matrix = self._create_matrix(phi, theta, psi, axes_order)

     92         result = np.dot(matrix, inp)

     93         a, b = self.cartesian2spherical(*result)



~/anaconda3/lib/python3.7/site-packages/astropy/modeling/rotations.py in _create_matrix(self, phi, theta, psi, axes_order)

     47             if isinstance(angle, u.Quantity):

     48                 angle = angle.value

---> 49             angle = angle.item()

     50             matrices.append(rotation_matrix(angle, axis, unit=u.rad))

     51         result = matrix_product(*matrices[::-1])



AttributeError: 'float' object has no attribute 'item'


I don't understand why it is expecting `angle` to have the `item` attribute.

Does anyone know what I'm doing wrong? Any help would be much appreciated.

Thanks!
M.




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From martinberoiz at gmail.com  Tue Sep 10 08:54:36 2019
From: martinberoiz at gmail.com (Martin Beroiz)
Date: Tue, 10 Sep 2019 07:54:36 -0500
Subject: [AstroPy] question about RotateNative2Celestial
In-Reply-To: <625553F3-78F7-40F2-AA2C-931ECB9FC5A0@stsci.edu>
References: <a489a51a-02cf-4ec1-808e-d580306734e5@Spark>
 <1346a89d-3f77-4242-a39e-a071f7524cb7@Spark>
 <625553F3-78F7-40F2-AA2C-931ECB9FC5A0@stsci.edu>
Message-ID: <a4afe02f-2bee-45e4-a578-8c16cab18cd9@Spark>

Hi Nadia,

Oh, I see! That worked well.

Thank you very much.
M.
On Sep 10, 2019, 6:40 AM -0500, Nadia Dencheva <dencheva at stsci.edu>, wrote:
> Hi Martin,
>
> Astropy.modeling models have a ?__call__ method and are supposed to be called as functions.
> The ?__call__? method does some additional reformatting of inputs and outputs (basically using
> arrays internally).
>
> Try calling it like this:
>
> n2c(x, y)
>
> Cheers,
> Nadia
>
> From: AstroPy <astropy-bounces+dencheva=stsci.edu at python.org> on behalf of Martin Beroiz <martinberoiz at gmail.com>
> Reply-To: Astronomical Python mailing list <astropy at python.org>
> Date: Monday, September 9, 2019 at 11:20 AM
> To: "astropy at python.org" <astropy at python.org>
> Subject: [AstroPy] question about RotateNative2Celestial
>
> Hello,
>
> I?m toying a little with WCS and?the functions on astropy.modeling.rotations.
> I?m not sure if I found a bug or if I don?t understand yet the API for?RotateNative2Celestial
> Here?s the small example that I came up with and the traceback I get
>
> from astropy.modeling import rotations as r
> lon = 100.00
> lat = -63.00
> alpha_c = 100.00
> delta_c = -63.00
> lon_pole = 180.0
>
> n2c = r.RotateNative2Celestial(lon, lat, lon_pole)
> n2c.evaluate(0., 90., lon, lat, lon_pole)
>
> ---------------------------------------------------------------------------
> AttributeError                            Traceback (most recent call last)
> <ipython-input-4-0a1e86053054> in <module>
> ----> 1 n2c.evaluate(0., 90., lon, lat, lon_pole)
> ~/anaconda3/lib/python3.7/site-packages/astropy/modeling/rotations.py in evaluate(self, phi_N, theta_N, lon, lat, lon_pole)
>    252         theta = - (np.pi / 2 - lat)
>    253         psi = -(np.pi / 2 + lon)
> --> 254         alpha_C, delta_C = super()._evaluate(phi_N, theta_N, phi, theta, psi)
>    255         return alpha_C, delta_C
>    256
> ~/anaconda3/lib/python3.7/site-packages/astropy/modeling/rotations.py in _evaluate(self, phi, theta, lon, lat, lon_pole)
>    183     def _evaluate(self, phi, theta, lon, lat, lon_pole):
>    184         alpha, delta = super().evaluate(phi, theta, lon, lat, lon_pole,
> --> 185                                         self.axes_order)
>    186         mask = alpha < 0
>    187         if isinstance(mask, np.ndarray):
> ~/anaconda3/lib/python3.7/site-packages/astropy/modeling/rotations.py in evaluate(self, alpha, delta, phi, theta, psi, axes_order)
>     89             shape = alpha.shape
>     90         inp = self.spherical2cartesian(alpha, delta)
> ---> 91         matrix = self._create_matrix(phi, theta, psi, axes_order)
>     92         result = np.dot(matrix, inp)
>     93         a, b = self.cartesian2spherical(*result)
> ~/anaconda3/lib/python3.7/site-packages/astropy/modeling/rotations.py in _create_matrix(self, phi, theta, psi, axes_order)
>     47             if isinstance(angle, u.Quantity):
>     48                 angle = angle.value
> ---> 49             angle = angle.item()
>     50             matrices.append(rotation_matrix(angle, axis, unit=u.rad))
>     51         result = matrix_product(*matrices[::-1])
> AttributeError: 'float' object has no attribute 'item'
>
>
> I don't understand why it is expecting `angle` to have the `item` attribute.
>
> Does anyone know what I'm doing wrong? Any help would be much appreciated.
>
> Thanks!
> M.
>
>
>
>
> _______________________________________________
> AstroPy mailing list
> AstroPy at python.org
> https://mail.python.org/mailman/listinfo/astropy
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From mburger at stsci.edu  Tue Sep 10 09:12:57 2019
From: mburger at stsci.edu (Matthew Burger)
Date: Tue, 10 Sep 2019 13:12:57 +0000
Subject: [AstroPy] Solar System ephemerides in astropy.coordinates
Message-ID: <51BA6907-C232-4167-AAB7-3078BC6609E1@contoso.com>

I?m trying to use astropy.coordinates.solar_system_ephemeris to calculate the RA and Dec of other bodies besides planets. Is this possible? I know which JPL SPICE kernels I want to use, but I can?t load them. If I specify another kernel with a url (e.g., https://naif.jpl.nasa.gov/pub/naif/generic_kernels/spk/satellites/jup310.bsp), it downloads the file but can?t use it.

I?m using astropy 3.2.1 with python 3.7.4.

Thanks,
Matt

*************************************************************
Matthew Burger
Archive Scientist
Data Processing & Archive Services (DPAS), Deputy Branch Manager
Space Telescope Science Institute
mburger at stsci.edu<mailto:mburger at stsci.edu>
410/338-6810
*************************************************************


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From juanlu001 at gmail.com  Tue Sep 10 09:41:29 2019
From: juanlu001 at gmail.com (Juan Luis Cano)
Date: Tue, 10 Sep 2019 15:41:29 +0200
Subject: [AstroPy] Solar System ephemerides in astropy.coordinates
In-Reply-To: <51BA6907-C232-4167-AAB7-3078BC6609E1@contoso.com>
References: <51BA6907-C232-4167-AAB7-3078BC6609E1@contoso.com>
Message-ID: <CAFmivUVK9i4ELn80L2zj8Gf+ub24Q3O8GRffiSci+DstYkxBdw@mail.gmail.com>

Hello Matt,

The SPK segments are hardcoded (see links and comments in
https://github.com/astropy/astropy/issues/6472) so, unless I'm mistaken, I
don't think this is something that can be easily done in Astropy. I would
be interested to see this happening though.

As an alternative, you might be interested in checking SpiceyPy
https://github.com/AndrewAnnex/SpiceyPy/ (installable with pip and
conda-forge) and try to combine it with astropy.coordinates.

Regards,

On Tue, Sep 10, 2019 at 3:28 PM Matthew Burger <mburger at stsci.edu> wrote:

> I?m trying to use astropy.coordinates.solar_system_ephemeris to calculate
> the RA and Dec of other bodies besides planets. Is this possible? I know
> which JPL SPICE kernels I want to use, but I can?t load them. If I specify
> another kernel with a url (e.g.,
> https://naif.jpl.nasa.gov/pub/naif/generic_kernels/spk/satellites/jup310.bsp),
> it downloads the file but can?t use it.
>
>
>
> I?m using astropy 3.2.1 with python 3.7.4.
>
>
>
> Thanks,
>
> Matt
>
>
>
> *************************************************************
>
> Matthew Burger
>
> Archive Scientist
>
> Data Processing & Archive Services (DPAS), Deputy Branch Manager
>
> Space Telescope Science Institute
>
> mburger at stsci.edu
>
> 410/338-6810
>
> *************************************************************
>
>
>
>
> _______________________________________________
> AstroPy mailing list
> AstroPy at python.org
> https://mail.python.org/mailman/listinfo/astropy
>


-- 
Juan Luis Cano
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From Andrew.Williams at curtin.edu.au  Tue Sep 10 10:22:09 2019
From: Andrew.Williams at curtin.edu.au (Andrew Williams)
Date: Tue, 10 Sep 2019 14:22:09 +0000
Subject: [AstroPy] Solar System ephemerides in astropy.coordinates
In-Reply-To: <CAFmivUVK9i4ELn80L2zj8Gf+ub24Q3O8GRffiSci+DstYkxBdw@mail.gmail.com>
References: <51BA6907-C232-4167-AAB7-3078BC6609E1@contoso.com>
 <CAFmivUVK9i4ELn80L2zj8Gf+ub24Q3O8GRffiSci+DstYkxBdw@mail.gmail.com>
Message-ID: <013e6789-fca9-de5a-c79a-642e06b00030@curtin.edu.au>


Hi Matt, I'd give skyfield (https://rhodesmill.org/skyfield/) a try - 
it's a complete rewrite of pyephem by the original package maintainer. 
It's very fast, uses the JPL ephemeris as well as parsing satellite 
TLEs, and plays nicely with astropy objects (converting times and 
coordinates to and from astropy Time and SkyCoord objects).

Andrew

On 2019-09-10 9:41 PM, Juan Luis Cano wrote:
> Hello Matt,
> 
> The SPK segments are hardcoded (see links and comments in 
> https://github.com/astropy/astropy/issues/6472) so, unless I'm mistaken, 
> I don't think this is something that can be easily done in Astropy. I 
> would be interested to see this happening though.
> 
> As an alternative, you might be interested in checking SpiceyPy 
> https://github.com/AndrewAnnex/SpiceyPy/ (installable with pip and 
> conda-forge) and try to combine it with astropy.coordinates.
> 
> Regards,
> 
> On Tue, Sep 10, 2019 at 3:28 PM Matthew Burger <mburger at stsci.edu 
> <mailto:mburger at stsci.edu>> wrote:
> 
>     I?m trying to use astropy.coordinates.solar_system_ephemeris to
>     calculate the RA and Dec of other bodies besides planets. Is this
>     possible? I know which JPL SPICE kernels I want to use, but I can?t
>     load them. If I specify another kernel with a url (e.g.,
>     https://naif.jpl.nasa.gov/pub/naif/generic_kernels/spk/satellites/jup310.bsp),
>     it downloads the file but can?t use it.____
> 
>     __ __
> 
>     I?m using astropy 3.2.1 with python 3.7.4.____
> 
>     __ __
> 
>     Thanks,____
> 
>     Matt____
> 
>     __ __
> 
>     *************************************************************____
> 
>     Matthew Burger____
> 
>     Archive Scientist____
> 
>     Data Processing & Archive Services (DPAS), Deputy Branch Manager____
> 
>     Space Telescope Science Institute____
> 
>     mburger at stsci.edu <mailto:mburger at stsci.edu>____
> 
>     410/338-6810____
> 
>     *************************************************************____
> 
>     __ __
> 
>     __ __
> 
>     _______________________________________________
>     AstroPy mailing list
>     AstroPy at python.org <mailto:AstroPy at python.org>
>     https://mail.python.org/mailman/listinfo/astropy
> 
> 
> 
> -- 
> Juan Luis Cano
> 
> _______________________________________________
> AstroPy mailing list
> AstroPy at python.org
> https://mail.python.org/mailman/listinfo/astropy
> 


From mburger at stsci.edu  Tue Sep 10 10:28:59 2019
From: mburger at stsci.edu (Matthew Burger)
Date: Tue, 10 Sep 2019 14:28:59 +0000
Subject: [AstroPy] AstroPy Digest, Vol 156, Issue 8
In-Reply-To: <mailman.4235.1568125408.30343.astropy@python.org>
References: <mailman.4235.1568125408.30343.astropy@python.org>
Message-ID: <75E5799A-7B25-4EA0-AC97-2851E4F4C140@stsci.edu>

Thanks for these suggestions. I've used spicepy, but astropy.coordinates was easier (for planets) and didn't add any dependencies. I haven't looked at skyfield yet.

Matt    

    
    Message: 2
    Date: Tue, 10 Sep 2019 15:41:29 +0200
    From: Juan Luis Cano <juanlu001 at gmail.com>
    To: Astronomical Python mailing list <astropy at python.org>
    Subject: Re: [AstroPy] Solar System ephemerides in astropy.coordinates
    Message-ID:
    	<CAFmivUVK9i4ELn80L2zj8Gf+ub24Q3O8GRffiSci+DstYkxBdw at mail.gmail.com>
    Content-Type: text/plain; charset="utf-8"
    
    Hello Matt,
    
    The SPK segments are hardcoded (see links and comments in
    https://github.com/astropy/astropy/issues/6472) so, unless I'm mistaken, I
    don't think this is something that can be easily done in Astropy. I would
    be interested to see this happening though.
    
    As an alternative, you might be interested in checking SpiceyPy
    https://github.com/AndrewAnnex/SpiceyPy/ (installable with pip and
    conda-forge) and try to combine it with astropy.coordinates.
    
    Regards,
    
    On Tue, Sep 10, 2019 at 3:28 PM Matthew Burger <mburger at stsci.edu> wrote:
    
    > I?m trying to use astropy.coordinates.solar_system_ephemeris to calculate
    > the RA and Dec of other bodies besides planets. Is this possible? I know
    > which JPL SPICE kernels I want to use, but I can?t load them. If I specify
    > another kernel with a url (e.g.,
    > https://naif.jpl.nasa.gov/pub/naif/generic_kernels/spk/satellites/jup310.bsp),
    > it downloads the file but can?t use it.
    >
    >
    >
    > I?m using astropy 3.2.1 with python 3.7.4.
    >
    >
    >
    > Thanks,
    >
    > Matt
    >
    >
    >
    > *************************************************************
    >
    > Matthew Burger
    >
    > Archive Scientist
    >
    > Data Processing & Archive Services (DPAS), Deputy Branch Manager
    >
    > Space Telescope Science Institute
    >
    > mburger at stsci.edu
    >
    > 410/338-6810
    >
    > *************************************************************
    >
    >
    >
    >
    > _______________________________________________
    > AstroPy mailing list
    > AstroPy at python.org
    > https://mail.python.org/mailman/listinfo/astropy
    >
    
    
    -- 
    Juan Luis Cano
    -------------- next part --------------
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    ------------------------------
    
    Message: 3
    Date: Tue, 10 Sep 2019 14:22:09 +0000
    From: Andrew Williams <Andrew.Williams at curtin.edu.au>
    To: Astronomical Python mailing list <astropy at python.org>
    Subject: Re: [AstroPy] Solar System ephemerides in astropy.coordinates
    Message-ID: <013e6789-fca9-de5a-c79a-642e06b00030 at curtin.edu.au>
    Content-Type: text/plain; charset="utf-8"
    
    
    Hi Matt, I'd give skyfield (https://rhodesmill.org/skyfield/) a try - 
    it's a complete rewrite of pyephem by the original package maintainer. 
    It's very fast, uses the JPL ephemeris as well as parsing satellite 
    TLEs, and plays nicely with astropy objects (converting times and 
    coordinates to and from astropy Time and SkyCoord objects).
    
    Andrew
    
    On 2019-09-10 9:41 PM, Juan Luis Cano wrote:
    > Hello Matt,
    > 
    > The SPK segments are hardcoded (see links and comments in 
    > https://github.com/astropy/astropy/issues/6472) so, unless I'm mistaken, 
    > I don't think this is something that can be easily done in Astropy. I 
    > would be interested to see this happening though.
    > 
    > As an alternative, you might be interested in checking SpiceyPy 
    > https://github.com/AndrewAnnex/SpiceyPy/ (installable with pip and 
    > conda-forge) and try to combine it with astropy.coordinates.
    > 
    > Regards,
    > 
    > On Tue, Sep 10, 2019 at 3:28 PM Matthew Burger <mburger at stsci.edu 
    > <mailto:mburger at stsci.edu>> wrote:
    > 
    >     I?m trying to use astropy.coordinates.solar_system_ephemeris to
    >     calculate the RA and Dec of other bodies besides planets. Is this
    >     possible? I know which JPL SPICE kernels I want to use, but I can?t
    >     load them. If I specify another kernel with a url (e.g.,
    >     https://naif.jpl.nasa.gov/pub/naif/generic_kernels/spk/satellites/jup310.bsp),
    >     it downloads the file but can?t use it.____
    > 
    >     __ __
    > 
    >     I?m using astropy 3.2.1 with python 3.7.4.____
    > 
    >     __ __
    > 
    >     Thanks,____
    > 
    >     Matt____
    > 
    >     __ __
    > 
    >     *************************************************************____
    > 
    >     Matthew Burger____
    > 
    >     Archive Scientist____
    > 
    >     Data Processing & Archive Services (DPAS), Deputy Branch Manager____
    > 
    >     Space Telescope Science Institute____
    > 
    >     mburger at stsci.edu <mailto:mburger at stsci.edu>____
    > 
    >     410/338-6810____
    > 
    >     *************************************************************____
    > 
    >     __ __
    > 
    >     __ __
    > 
    >     _______________________________________________
    >     AstroPy mailing list
    >     AstroPy at python.org <mailto:AstroPy at python.org>
    >     https://mail.python.org/mailman/listinfo/astropy
    > 
    > 
    > 
    > -- 
    > Juan Luis Cano
    > 
    > _______________________________________________
    > AstroPy mailing list
    > AstroPy at python.org
    > https://mail.python.org/mailman/listinfo/astropy
    > 
    
    
    ------------------------------
    
    Subject: Digest Footer
    
    _______________________________________________
    AstroPy mailing list
    AstroPy at python.org
    https://mail.python.org/mailman/listinfo/astropy
    
    
    ------------------------------
    
    End of AstroPy Digest, Vol 156, Issue 8
    ***************************************
    


From jgv.home at gmail.com  Tue Sep 10 10:44:23 2019
From: jgv.home at gmail.com (j. vickroy)
Date: Tue, 10 Sep 2019 14:44:23 +0000
Subject: [AstroPy] Executable Script fitsheader
In-Reply-To: <CALykZjy7ScXQrTTeowjn3QvQC=o2HEcPjUJgHSYbdtc6LM5CPg@mail.gmail.com>
References: <CALykZjy7ScXQrTTeowjn3QvQC=o2HEcPjUJgHSYbdtc6LM5CPg@mail.gmail.com>
Message-ID: <emc17a8e4e-127c-44e3-ac4b-184fe281906e@jv-hp-desktop>

Sorry I do not have an answer, but since there have been no responses,  
here is what I'm seeing:

C:\Pictures\Astro>fitsheader *.fit
ERROR: [Errno 22] Invalid argument: '*.fit' 
[astropy.io.fits.scripts.fitsheader]

My setup is:
Microsoft Windows 10 fully-updatedPython 3.7.3astropy 3.2.1

When I have some time, I will look at fitsheader.py to see what the 
problem is.

Regards,
/jimv


On 9/9/2019 4:47:18 PM, "James Dull" <dull4.ja at gmail.com> wrote:

>I would like to extract header information from several hundred fits 
>files and put it into a csv file. I ran across the executable script 
>information fitsheader that appears to do just that. It works perfectly 
>for a single file. However, when I follow the online command for that 
>uses a wildcard so multiple files can be completed in a single pass I 
>get "unrecognized command"
>
>Something similar happens with the other scripts if I use a wildcard.
>
>I feel I'm missing something simple.
>
>The command I'm using is: fitsheader --table ascii.csv *.fits > 
>keywords.csv
>
>thanks
>Jim
>
>
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From sn.fotop at gmail.com  Tue Sep 10 10:55:28 2019
From: sn.fotop at gmail.com (Sotiria Fotopoulou)
Date: Tue, 10 Sep 2019 15:55:28 +0100
Subject: [AstroPy] Executable Script fitsheader
In-Reply-To: <CALykZjy7ScXQrTTeowjn3QvQC=o2HEcPjUJgHSYbdtc6LM5CPg@mail.gmail.com>
References: <CALykZjy7ScXQrTTeowjn3QvQC=o2HEcPjUJgHSYbdtc6LM5CPg@mail.gmail.com>
Message-ID: <CADj4VJTGgsZ+FnL1BGdDSkJfao-8-MG14FFcbx+Rk=g_ZkgnGA@mail.gmail.com>

Hi Jim,

your command works fine for me.
However, if you are in pinch and since it seems to work for a single file,
you could consider using a bash for loop like the following:
for FILE in *fits; do fitsheader --table ascii.csv $FILE >>
keywords.csv;done

Cheers,
Sotiria

On Mon, Sep 9, 2019 at 11:47 PM James Dull <dull4.ja at gmail.com> wrote:

> I would like to extract header information from several hundred fits files
> and put it into a csv file. I ran across the executable script information
> fitsheader that appears to do just that. It works perfectly for a single
> file. However, when I follow the online command for that uses a wildcard so
> multiple files can be completed in a single pass I get "unrecognized
> command"
>
> Something similar happens with the other scripts if I use a wildcard.
>
> I feel I'm missing something simple.
>
> The command I'm using is: fitsheader --table ascii.csv *.fits >
> keywords.csv
>
> thanks
> Jim
>
>
> _______________________________________________
> AstroPy mailing list
> AstroPy at python.org
> https://mail.python.org/mailman/listinfo/astropy
>
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From teuben at astro.umd.edu  Tue Sep 10 10:55:35 2019
From: teuben at astro.umd.edu (Peter Teuben)
Date: Tue, 10 Sep 2019 10:55:35 -0400
Subject: [AstroPy] Executable Script fitsheader
In-Reply-To: <emc17a8e4e-127c-44e3-ac4b-184fe281906e@jv-hp-desktop>
References: <CALykZjy7ScXQrTTeowjn3QvQC=o2HEcPjUJgHSYbdtc6LM5CPg@mail.gmail.com>
 <emc17a8e4e-127c-44e3-ac4b-184fe281906e@jv-hp-desktop>
Message-ID: <c16ff920-e6a0-3a99-e163-58979abcd81e@astro.umd.edu>

more than likely the argument is not fed via the glob module, as it 
seems to take *.fit as a literal, not a meta character. Looking at the 
documentation, it seems to support wildcards, but I should also note the 
documentation (in the source code) has 'errors', e.g. it lists

fitsheader --keyword NAXIS* filename.fits

as an example which I'm pretty sure doesn't work in all shells. In bash 
it will, since it's an overly controlling shell, or smart shell as some 
call it :-)? In csh, i can promise you, it won't work.

Since DOS does wildcards I believe, the other possibility could be that 
the command fitsheader doesn't point to the fitsheader.py from astropy, 
but from another package, since the name is pretty easy to come up with. 
Is there a "which" command in DOS ?

Does the command do the expected thing if you manually feed it more than 
one fit(s) file?

- peter


On 9/10/19 10:44 AM, j. vickroy wrote:
> Sorry I do not have an answer, but since there have been no responses, 
> ?here is what I'm seeing:
>
> C:\Pictures\Astro>fitsheader *.fit
> ERROR: [Errno 22] Invalid argument: '*.fit' 
> [astropy.io.fits.scripts.fitsheader]
>
> My setup is:
>
>   * Microsoft Windows 10 fully-updated
>   * Python 3.7.3
>   * astropy 3.2.1
>
>
> When I have some time, I will look at fitsheader.py to see what the 
> problem is.
>
> Regards,
> /jimv
>
>
> On 9/9/2019 4:47:18 PM, "James Dull" <dull4.ja at gmail.com 
> <mailto:dull4.ja at gmail.com>> wrote:
>
>> I would like to extract header information from several hundred fits 
>> files and put it into a csv file. I ran across the executable script 
>> information fitsheader that appears to do just that. It works 
>> perfectly for a single file. However, when I follow the online 
>> command for that uses a wildcard so multiple files can be completed 
>> in a single pass I get "unrecognized command"
>>
>> Something similar happens with the other scripts if I use a wildcard.
>>
>> I feel I'm missing something simple.
>>
>> The command I'm using is: fitsheader --table ascii.csv *.fits > 
>> keywords.csv
>>
>> thanks
>> Jim
>>
>>
>
> _______________________________________________
> AstroPy mailing list
> AstroPy at python.org
> https://mail.python.org/mailman/listinfo/astropy
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From jgv.home at gmail.com  Tue Sep 10 11:10:09 2019
From: jgv.home at gmail.com (j. vickroy)
Date: Tue, 10 Sep 2019 15:10:09 +0000
Subject: [AstroPy] Executable Script fitsheader
In-Reply-To: <CALykZjy7ScXQrTTeowjn3QvQC=o2HEcPjUJgHSYbdtc6LM5CPg@mail.gmail.com>
References: <CALykZjy7ScXQrTTeowjn3QvQC=o2HEcPjUJgHSYbdtc6LM5CPg@mail.gmail.com>
Message-ID: <em8bcf2a27-c726-4a0d-bc75-dd12746d5d8d@jv-hp-desktop>

As a quick followup ...

line 262 in function print_headers_traditional of 
...\Python\Python37\Lib\site-packages\astropy\io\fits\scripts\fitsheader.py 
is:

for idx, filename in enumerate(args.filename):  # support wildcards

filename, immediately after line 262, is simply "*.fit" which indicates 
args.filename has not been previously expanded if a wildcard has been 
specified.

At least that is the the behavior when running fitsheader.py from the 
C:\Windows\System32\cmd.exe shell on Microsoft Windows 10.

/jimv


On 9/9/2019 4:47:18 PM, "James Dull" <dull4.ja at gmail.com> wrote:

>I would like to extract header information from several hundred fits 
>files and put it into a csv file. I ran across the executable script 
>information fitsheader that appears to do just that. It works perfectly 
>for a single file. However, when I follow the online command for that 
>uses a wildcard so multiple files can be completed in a single pass I 
>get "unrecognized command"
>
>Something similar happens with the other scripts if I use a wildcard.
>
>I feel I'm missing something simple.
>
>The command I'm using is: fitsheader --table ascii.csv *.fits > 
>keywords.csv
>
>thanks
>Jim
>
>
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From dull4.ja at gmail.com  Tue Sep 10 13:04:01 2019
From: dull4.ja at gmail.com (James Dull)
Date: Tue, 10 Sep 2019 11:04:01 -0600
Subject: [AstroPy] Executable Script fitsheader
In-Reply-To: <emc17a8e4e-127c-44e3-ac4b-184fe281906e@jv-hp-desktop>
References: <CALykZjy7ScXQrTTeowjn3QvQC=o2HEcPjUJgHSYbdtc6LM5CPg@mail.gmail.com>
 <emc17a8e4e-127c-44e3-ac4b-184fe281906e@jv-hp-desktop>
Message-ID: <CALykZjyuNWOffD1HF0a86L9V2qx2cSW1XZh9WBj9j0BWMX-KXw@mail.gmail.com>

Thanks for all of the input.

I should have provided more information. I have the same set-up as
described below and get the same error.
I am using Windows 10.

Jim

On Tue, Sep 10, 2019 at 8:44 AM j. vickroy <jgv.home at gmail.com> wrote:

> Sorry I do not have an answer, but since there have been no responses,
>  here is what I'm seeing:
>
> C:\Pictures\Astro>fitsheader *.fit
> ERROR: [Errno 22] Invalid argument: '*.fit'
> [astropy.io.fits.scripts.fitsheader]
>
> My setup is:
>
>    - Microsoft Windows 10 fully-updated
>    - Python 3.7.3
>    - astropy 3.2.1
>
>
> When I have some time, I will look at fitsheader.py to see what the
> problem is.
>
> Regards,
> /jimv
>
>
> On 9/9/2019 4:47:18 PM, "James Dull" <dull4.ja at gmail.com> wrote:
>
> I would like to extract header information from several hundred fits files
> and put it into a csv file. I ran across the executable script information
> fitsheader that appears to do just that. It works perfectly for a single
> file. However, when I follow the online command for that uses a wildcard so
> multiple files can be completed in a single pass I get "unrecognized
> command"
>
> Something similar happens with the other scripts if I use a wildcard.
>
> I feel I'm missing something simple.
>
> The command I'm using is: fitsheader --table ascii.csv *.fits >
> keywords.csv
>
> thanks
> Jim
>
>
> _______________________________________________
> AstroPy mailing list
> AstroPy at python.org
> https://mail.python.org/mailman/listinfo/astropy
>
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From miguel.deval at gmail.com  Tue Sep 10 15:35:47 2019
From: miguel.deval at gmail.com (Miguel de Val-Borro)
Date: Tue, 10 Sep 2019 15:35:47 -0400
Subject: [AstroPy] Solar System ephemerides in astropy.coordinates
In-Reply-To: <013e6789-fca9-de5a-c79a-642e06b00030@curtin.edu.au>
References: <51BA6907-C232-4167-AAB7-3078BC6609E1@contoso.com>
 <CAFmivUVK9i4ELn80L2zj8Gf+ub24Q3O8GRffiSci+DstYkxBdw@mail.gmail.com>
 <013e6789-fca9-de5a-c79a-642e06b00030@curtin.edu.au>
Message-ID: <20190910193547.GA2233@tolstoy>

As yet another alternative, you could try the web interface 
to the JPL Horizons ephemerides system for solar-system bodies available
as an astroquery module:

https://astroquery.readthedocs.io/en/latest/jplhorizons/jplhorizons.html

Miguel

On Tue, Sep 10, 2019 at 02:22:09PM +0000, Andrew Williams wrote:
> 
> Hi Matt, I'd give skyfield (https://rhodesmill.org/skyfield/) a try - 
> it's a complete rewrite of pyephem by the original package maintainer. 
> It's very fast, uses the JPL ephemeris as well as parsing satellite 
> TLEs, and plays nicely with astropy objects (converting times and 
> coordinates to and from astropy Time and SkyCoord objects).
> 
> Andrew
> 
> On 2019-09-10 9:41 PM, Juan Luis Cano wrote:
> > Hello Matt,
> > 
> > The SPK segments are hardcoded (see links and comments in 
> > https://github.com/astropy/astropy/issues/6472) so, unless I'm mistaken, 
> > I don't think this is something that can be easily done in Astropy. I 
> > would be interested to see this happening though.
> > 
> > As an alternative, you might be interested in checking SpiceyPy 
> > https://github.com/AndrewAnnex/SpiceyPy/ (installable with pip and 
> > conda-forge) and try to combine it with astropy.coordinates.
> > 
> > Regards,
> > 
> > On Tue, Sep 10, 2019 at 3:28 PM Matthew Burger <mburger at stsci.edu 
> > <mailto:mburger at stsci.edu>> wrote:
> > 
> >     I?m trying to use astropy.coordinates.solar_system_ephemeris to
> >     calculate the RA and Dec of other bodies besides planets. Is this
> >     possible? I know which JPL SPICE kernels I want to use, but I can?t
> >     load them. If I specify another kernel with a url (e.g.,
> >     https://naif.jpl.nasa.gov/pub/naif/generic_kernels/spk/satellites/jup310.bsp),
> >     it downloads the file but can?t use it.____
> > 
> >     __ __
> > 
> >     I?m using astropy 3.2.1 with python 3.7.4.____
> > 
> >     __ __
> > 
> >     Thanks,____
> > 
> >     Matt____
> > 
> >     __ __
> > 
> >     *************************************************************____
> > 
> >     Matthew Burger____
> > 
> >     Archive Scientist____
> > 
> >     Data Processing & Archive Services (DPAS), Deputy Branch Manager____
> > 
> >     Space Telescope Science Institute____
> > 
> >     mburger at stsci.edu <mailto:mburger at stsci.edu>____
> > 
> >     410/338-6810____
> > 
> >     *************************************************************____
> > 
> >     __ __
> > 
> >     __ __
> > 
> >     _______________________________________________
> >     AstroPy mailing list
> >     AstroPy at python.org <mailto:AstroPy at python.org>
> >     https://mail.python.org/mailman/listinfo/astropy
> > 
> > 
> > 
> > -- 
> > Juan Luis Cano
> > 
> > _______________________________________________
> > 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

From simon at sconseil.fr  Tue Sep 10 16:54:33 2019
From: simon at sconseil.fr (Simon Conseil)
Date: Tue, 10 Sep 2019 22:54:33 +0200
Subject: [AstroPy] Executable Script fitsheader
In-Reply-To: <CALykZjyuNWOffD1HF0a86L9V2qx2cSW1XZh9WBj9j0BWMX-KXw@mail.gmail.com>
References: <CALykZjy7ScXQrTTeowjn3QvQC=o2HEcPjUJgHSYbdtc6LM5CPg@mail.gmail.com>
 <emc17a8e4e-127c-44e3-ac4b-184fe281906e@jv-hp-desktop>
 <CALykZjyuNWOffD1HF0a86L9V2qx2cSW1XZh9WBj9j0BWMX-KXw@mail.gmail.com>
Message-ID: <99edb966-2b63-5fc2-3f2f-1a18e3e1d0c7@sconseil.fr>

Hi,

Usually for this kind of script the shell takes care of the wildcard 
expansion (e.g. with bash/zsh on Linux/MacOS).

I don't know much about Windows, a quick search seems to show cmd.exe 
does not support wildcard expansion, but Powershell does 
(https://superuser.com/questions/460598/is-there-any-way-to-get-the-windows-cmd-shell-to-expand-wildcard-paths).

Simon


Le 10/09/2019 ? 19:04, James Dull a ?crit?:
> Thanks for all of the input.
>
> I should have provided more information. I have the same set-up as
> described below and get the same error.
> I am using Windows 10.
>
> Jim
>
> On Tue, Sep 10, 2019 at 8:44 AM j. vickroy <jgv.home at gmail.com> wrote:
>
>> Sorry I do not have an answer, but since there have been no responses,
>>   here is what I'm seeing:
>>
>> C:\Pictures\Astro>fitsheader *.fit
>> ERROR: [Errno 22] Invalid argument: '*.fit'
>> [astropy.io.fits.scripts.fitsheader]
>>
>> My setup is:
>>
>>     - Microsoft Windows 10 fully-updated
>>     - Python 3.7.3
>>     - astropy 3.2.1
>>
>>
>> When I have some time, I will look at fitsheader.py to see what the
>> problem is.
>>
>> Regards,
>> /jimv
>>
>>
>> On 9/9/2019 4:47:18 PM, "James Dull" <dull4.ja at gmail.com> wrote:
>>
>> I would like to extract header information from several hundred fits files
>> and put it into a csv file. I ran across the executable script information
>> fitsheader that appears to do just that. It works perfectly for a single
>> file. However, when I follow the online command for that uses a wildcard so
>> multiple files can be completed in a single pass I get "unrecognized
>> command"
>>
>> Something similar happens with the other scripts if I use a wildcard.
>>
>> I feel I'm missing something simple.
>>
>> The command I'm using is: fitsheader --table ascii.csv *.fits >
>> keywords.csv
>>
>> thanks
>> Jim
>>
>>
>> _______________________________________________
>> 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 pdzwig at summaventures.com  Wed Sep 11 05:38:54 2019
From: pdzwig at summaventures.com (Peter Dzwig)
Date: Wed, 11 Sep 2019 11:38:54 +0200
Subject: [AstroPy] Executable Script fitsheader
In-Reply-To: <99edb966-2b63-5fc2-3f2f-1a18e3e1d0c7@sconseil.fr>
References: <CALykZjy7ScXQrTTeowjn3QvQC=o2HEcPjUJgHSYbdtc6LM5CPg@mail.gmail.com>
 <emc17a8e4e-127c-44e3-ac4b-184fe281906e@jv-hp-desktop>
 <CALykZjyuNWOffD1HF0a86L9V2qx2cSW1XZh9WBj9j0BWMX-KXw@mail.gmail.com>
 <99edb966-2b63-5fc2-3f2f-1a18e3e1d0c7@sconseil.fr>
Message-ID: <577d16f2-a641-17a9-8d54-51c369fe90f8@summaventures.com>

I tend to agree, although it is some time since I used Windows as a
serious compute environment, I seem to recall that cmd.exe lacked a lot
of the support that Powershell gives/gave better support.

Should this be reported to astropy as a bug?

Peter Dzwig

On 10/09/2019 22:54, Simon Conseil wrote:
> Hi,
> 
> Usually for this kind of script the shell takes care of the wildcard
> expansion (e.g. with bash/zsh on Linux/MacOS).
> 
> I don't know much about Windows, a quick search seems to show cmd.exe
> does not support wildcard expansion, but Powershell does
> (https://superuser.com/questions/460598/is-there-any-way-to-get-the-windows-cmd-shell-to-expand-wildcard-paths).
> 
> Simon
> 
> 
> Le 10/09/2019 ? 19:04, James Dull a ?crit?:
>> Thanks for all of the input.
>>
>> I should have provided more information. I have the same set-up as
>> described below and get the same error.
>> I am using Windows 10.
>>
>> Jim
>>
>> On Tue, Sep 10, 2019 at 8:44 AM j. vickroy <jgv.home at gmail.com> wrote:
>>
>>> Sorry I do not have an answer, but since there have been no responses,
>>>  here is what I'm seeing:
>>>
>>> C:\Pictures\Astro>fitsheader *.fit
>>> ERROR: [Errno 22] Invalid argument: '*.fit'
>>> [astropy.io.fits.scripts.fitsheader]
>>>
>>> My setup is:
>>>
>>>    - Microsoft Windows 10 fully-updated
>>>    - Python 3.7.3
>>>    - astropy 3.2.1
>>>
>>>
>>> When I have some time, I will look at fitsheader.py to see what the
>>> problem is.
>>>
>>> Regards,
>>> /jimv
>>>
>>>
>>> On 9/9/2019 4:47:18 PM, "James Dull" <dull4.ja at gmail.com> wrote:
>>>
>>> I would like to extract header information from several hundred fits files
>>> and put it into a csv file. I ran across the executable script information
>>> fitsheader that appears to do just that. It works perfectly for a single
>>> file. However, when I follow the online command for that uses a wildcard so
>>> multiple files can be completed in a single pass I get "unrecognized
>>> command"
>>>
>>> Something similar happens with the other scripts if I use a wildcard.
>>>
>>> I feel I'm missing something simple.
>>>
>>> The command I'm using is: fitsheader --table ascii.csv *.fits >
>>> keywords.csv
>>>
>>> thanks
>>> Jim
>>>
>>>
>>> _______________________________________________
>>> 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
> 
> _______________________________________________
> AstroPy mailing list
> AstroPy at python.org
> https://mail.python.org/mailman/listinfo/astropy
> 

-- 

Dr. Peter Dzwig

From sn.fotop at gmail.com  Wed Sep 11 05:55:16 2019
From: sn.fotop at gmail.com (Sotiria Fotopoulou)
Date: Wed, 11 Sep 2019 10:55:16 +0100
Subject: [AstroPy] Executable Script fitsheader
In-Reply-To: <577d16f2-a641-17a9-8d54-51c369fe90f8@summaventures.com>
References: <CALykZjy7ScXQrTTeowjn3QvQC=o2HEcPjUJgHSYbdtc6LM5CPg@mail.gmail.com>
 <emc17a8e4e-127c-44e3-ac4b-184fe281906e@jv-hp-desktop>
 <CALykZjyuNWOffD1HF0a86L9V2qx2cSW1XZh9WBj9j0BWMX-KXw@mail.gmail.com>
 <99edb966-2b63-5fc2-3f2f-1a18e3e1d0c7@sconseil.fr>
 <577d16f2-a641-17a9-8d54-51c369fe90f8@summaventures.com>
Message-ID: <CADj4VJRxbXCe2V00a6KJDrGXaxEJefzKC7TdJk9X716fEsWdzg@mail.gmail.com>

I don't think the wildcard expansion is astropy's shortcoming.
Perhaps an issue should be raised for a more informative error message or a
suggestion to be printed to use powershell.

Cheers,
Sotiria

On Wed, Sep 11, 2019 at 10:45 AM Peter Dzwig <pdzwig at summaventures.com>
wrote:

> I tend to agree, although it is some time since I used Windows as a
> serious compute environment, I seem to recall that cmd.exe lacked a lot
> of the support that Powershell gives/gave better support.
>
> Should this be reported to astropy as a bug?
>
> Peter Dzwig
>
> On 10/09/2019 22:54, Simon Conseil wrote:
> > Hi,
> >
> > Usually for this kind of script the shell takes care of the wildcard
> > expansion (e.g. with bash/zsh on Linux/MacOS).
> >
> > I don't know much about Windows, a quick search seems to show cmd.exe
> > does not support wildcard expansion, but Powershell does
> > (
> https://superuser.com/questions/460598/is-there-any-way-to-get-the-windows-cmd-shell-to-expand-wildcard-paths
> ).
> >
> > Simon
> >
> >
> > Le 10/09/2019 ? 19:04, James Dull a ?crit :
> >> Thanks for all of the input.
> >>
> >> I should have provided more information. I have the same set-up as
> >> described below and get the same error.
> >> I am using Windows 10.
> >>
> >> Jim
> >>
> >> On Tue, Sep 10, 2019 at 8:44 AM j. vickroy <jgv.home at gmail.com> wrote:
> >>
> >>> Sorry I do not have an answer, but since there have been no responses,
> >>>  here is what I'm seeing:
> >>>
> >>> C:\Pictures\Astro>fitsheader *.fit
> >>> ERROR: [Errno 22] Invalid argument: '*.fit'
> >>> [astropy.io.fits.scripts.fitsheader]
> >>>
> >>> My setup is:
> >>>
> >>>    - Microsoft Windows 10 fully-updated
> >>>    - Python 3.7.3
> >>>    - astropy 3.2.1
> >>>
> >>>
> >>> When I have some time, I will look at fitsheader.py to see what the
> >>> problem is.
> >>>
> >>> Regards,
> >>> /jimv
> >>>
> >>>
> >>> On 9/9/2019 4:47:18 PM, "James Dull" <dull4.ja at gmail.com> wrote:
> >>>
> >>> I would like to extract header information from several hundred fits
> files
> >>> and put it into a csv file. I ran across the executable script
> information
> >>> fitsheader that appears to do just that. It works perfectly for a
> single
> >>> file. However, when I follow the online command for that uses a
> wildcard so
> >>> multiple files can be completed in a single pass I get "unrecognized
> >>> command"
> >>>
> >>> Something similar happens with the other scripts if I use a wildcard.
> >>>
> >>> I feel I'm missing something simple.
> >>>
> >>> The command I'm using is: fitsheader --table ascii.csv *.fits >
> >>> keywords.csv
> >>>
> >>> thanks
> >>> Jim
> >>>
> >>>
> >>> _______________________________________________
> >>> 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
> >
> > _______________________________________________
> > AstroPy mailing list
> > AstroPy at python.org
> > https://mail.python.org/mailman/listinfo/astropy
> >
>
> --
>
> Dr. Peter Dzwig
> _______________________________________________
> AstroPy mailing list
> AstroPy at python.org
> https://mail.python.org/mailman/listinfo/astropy
>
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From jgv.home at gmail.com  Wed Sep 11 09:54:29 2019
From: jgv.home at gmail.com (j. vickroy)
Date: Wed, 11 Sep 2019 13:54:29 +0000
Subject: [AstroPy] Executable Script fitsheader
In-Reply-To: <CADj4VJRxbXCe2V00a6KJDrGXaxEJefzKC7TdJk9X716fEsWdzg@mail.gmail.com>
References: <CALykZjy7ScXQrTTeowjn3QvQC=o2HEcPjUJgHSYbdtc6LM5CPg@mail.gmail.com>
 <emc17a8e4e-127c-44e3-ac4b-184fe281906e@jv-hp-desktop>
 <CALykZjyuNWOffD1HF0a86L9V2qx2cSW1XZh9WBj9j0BWMX-KXw@mail.gmail.com>
 <99edb966-2b63-5fc2-3f2f-1a18e3e1d0c7@sconseil.fr>
 <577d16f2-a641-17a9-8d54-51c369fe90f8@summaventures.com>
 <CADj4VJRxbXCe2V00a6KJDrGXaxEJefzKC7TdJk9X716fEsWdzg@mail.gmail.com>
Message-ID: <emb59a87fc-4fc8-4a95-b76d-23f9c4472d43@jv-hp-desktop>

Sine python provides the glob module, I believe these astropy scripts 
should not assume command-line expansion of wildcards.

At a minimum, their documentation should be updated to state the 
implicit assumption that wildcard expansion is left to the shell, and 
that, in particular, they do not work as advertised when used in 
Microsoft Windows cmd.exe.

Regards,
/jimv

On 9/11/2019 3:55:16 AM, "Sotiria Fotopoulou" <sn.fotop at gmail.com> 
wrote:

>I don't think the wildcard expansion is astropy's shortcoming.
>Perhaps an issue should be raised for a more informative error message 
>or a suggestion to be printed to use powershell.
>
>Cheers,
>Sotiria
>
>On Wed, Sep 11, 2019 at 10:45 AM Peter Dzwig <pdzwig at summaventures.com> 
>wrote:
>>I tend to agree, although it is some time since I used Windows as a
>>serious compute environment, I seem to recall that cmd.exe lacked a 
>>lot
>>of the support that Powershell gives/gave better support.
>>
>>Should this be reported to astropy as a bug?
>>
>>Peter Dzwig
>>
>>On 10/09/2019 22:54, Simon Conseil wrote:
>> > Hi,
>> >
>> > Usually for this kind of script the shell takes care of the wildcard
>> > expansion (e.g. with bash/zsh on Linux/MacOS).
>> >
>> > I don't know much about Windows, a quick search seems to show 
>>cmd.exe
>> > does not support wildcard expansion, but Powershell does
>> > 
>>(https://superuser.com/questions/460598/is-there-any-way-to-get-the-windows-cmd-shell-to-expand-wildcard-paths).
>> >
>> > Simon
>> >
>> >
>> > Le 10/09/2019 ? 19:04, James Dull a ?crit :
>> >> Thanks for all of the input.
>> >>
>> >> I should have provided more information. I have the same set-up as
>> >> described below and get the same error.
>> >> I am using Windows 10.
>> >>
>> >> Jim
>> >>
>> >> On Tue, Sep 10, 2019 at 8:44 AM j. vickroy <jgv.home at gmail.com> 
>>wrote:
>> >>
>> >>> Sorry I do not have an answer, but since there have been no 
>>responses,
>> >>>  here is what I'm seeing:
>> >>>
>> >>> C:\Pictures\Astro>fitsheader *.fit
>> >>> ERROR: [Errno 22] Invalid argument: '*.fit'
>> >>> [astropy.io.fits.scripts.fitsheader]
>> >>>
>> >>> My setup is:
>> >>>
>> >>>    - Microsoft Windows 10 fully-updated
>> >>>    - Python 3.7.3
>> >>>    - astropy 3.2.1
>> >>>
>> >>>
>> >>> When I have some time, I will look at fitsheader.py to see what 
>>the
>> >>> problem is.
>> >>>
>> >>> Regards,
>> >>> /jimv
>> >>>
>> >>>
>> >>> On 9/9/2019 4:47:18 PM, "James Dull" <dull4.ja at gmail.com> wrote:
>> >>>
>> >>> I would like to extract header information from several hundred 
>>fits files
>> >>> and put it into a csv file. I ran across the executable script 
>>information
>> >>> fitsheader that appears to do just that. It works perfectly for a 
>>single
>> >>> file. However, when I follow the online command for that uses a 
>>wildcard so
>> >>> multiple files can be completed in a single pass I get 
>>"unrecognized
>> >>> command"
>> >>>
>> >>> Something similar happens with the other scripts if I use a 
>>wildcard.
>> >>>
>> >>> I feel I'm missing something simple.
>> >>>
>> >>> The command I'm using is: fitsheader --table ascii.csv *.fits >
>> >>> keywords.csv
>> >>>
>> >>> thanks
>> >>> Jim
>> >>>
>> >>>
>> >>> _______________________________________________
>> >>> 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
>> >
>> > _______________________________________________
>> > AstroPy mailing list
>> > AstroPy at python.org
>> > https://mail.python.org/mailman/listinfo/astropy
>> >
>>
>>--
>>
>>Dr. Peter Dzwig
>>_______________________________________________
>>AstroPy mailing list
>>AstroPy at python.org
>>https://mail.python.org/mailman/listinfo/astropy
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From bsipocz at gmail.com  Thu Sep 12 14:19:25 2019
From: bsipocz at gmail.com (Brigitta Sipocz)
Date: Thu, 12 Sep 2019 19:19:25 +0100
Subject: [AstroPy] astroML workshop at the 235th AAS Meeting
Message-ID: <CAEjJ3fgZFi-tq1BF_7AEC_gCeayjJ5YKWr08W4t_+1m78CCuZw@mail.gmail.com>

Dear All,

Registration is open for the upcoming astroML workshop
<http://www.astroml.org/workshops/AAS235.html>. The workshop will be held
at the AAS winter meeting, Monday, 6 January 2020.

This workshop will introduce the astronomical community to the 2nd edition
of the book *Statistics, Data Mining, and Machine Learning in Astronomy*
and the associated software package astroML. The goal is to introduce
participants to a variety of statistical and machine learning tools
available within the open source astroML library. The format will be
interactive, including short presentations on different machine learning
methodologies followed by instructor-guided, Jupyter notebook based
tutorials. In these tutorial sessions participants will be able to try out
the tools and to ask questions from expert users and developers.

Our primary focus will be on the new material and applications in the 2nd
edition of the book. These include:

   -

   Traditional machine learning techniques for density estimation,
   -

   Approximate Bayesian computation,
   -

   Hierarchical Bayesian models,
   -

   Autoencoders as tools for data compression,
   -

   Deep learning and convolutional neural networks.

In each tutorial example applications will be based on astronomical use
cases and data sets. At the end of the workshop we will present a roadmap
for future developments in astroML.

This workshop is suitable for those with existing Python knowledge,
including familiarity with the core packages in the numerical Python
ecosystem such as numpy, scipy, scikit-learn, and matplotlib.
Registration is open on the website of the meeting:
https://aas.org/meetings/aas235


On behalf of the organizers,
 Brigitta Sip?cz
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From peridot.faceted at gmail.com  Wed Sep 18 12:41:47 2019
From: peridot.faceted at gmail.com (Anne Archibald)
Date: Wed, 18 Sep 2019 18:41:47 +0200
Subject: [AstroPy] Instructions for using dev tools
Message-ID: <CANm_+Zo2e4Zo+G-0aKTdY1_Tg0w_iCdhF4rD7jNgXZeVRtZvLw@mail.gmail.com>

Hi,

I have been working on a couple of astropy pull requests, and I would like
to take advantage of various development tools, but I can't find any
instructions and they don't seem to do the right thing by default.

* How do I run flake8 to see if my files meet the coding standards? If I
just run flake8 from the root directory I am submerged in a blizzard of
warnings from files I have never touched. The same is true of python
setup.py flake8. I see that there is a CI run that runs flake8 with all
sorts of warnings turned off, but it's arranged through an environment
variable so there's no easy way for me to use that (should I?). I can run
flake8-diff, but again it complains about all sorts of things - often lines
that are too long - that are clearly acceptable in astropy source code. Is
the current situation because there are two levels of flake8 compliance -
one that is needed to allow building at all, and a better one new code
should meet?

* How do I clear out the test environment? I find with python setup.py test
astropy keeps running tests left over from another branch. I have no idea
where these are stored, perhaps in the virtualenv of the installed package?

I am happy to add the correct instructions to CONTRIBUTING.rst, when I find
out what they are.

Thanks,
Anne
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From aldcroft at head.cfa.harvard.edu  Wed Sep 18 14:06:08 2019
From: aldcroft at head.cfa.harvard.edu (Aldcroft, Thomas)
Date: Wed, 18 Sep 2019 14:06:08 -0400
Subject: [AstroPy] Instructions for using dev tools
In-Reply-To: <CANm_+Zo2e4Zo+G-0aKTdY1_Tg0w_iCdhF4rD7jNgXZeVRtZvLw@mail.gmail.com>
References: <CANm_+Zo2e4Zo+G-0aKTdY1_Tg0w_iCdhF4rD7jNgXZeVRtZvLw@mail.gmail.com>
Message-ID: <CAMtEP6zcGaNFSu33e5OOX855V7m05BCXwvN6CM0++VdtTZkj3w@mail.gmail.com>

On Wed, Sep 18, 2019 at 12:42 PM Anne Archibald <peridot.faceted at gmail.com>
wrote:

> Hi,
>
> I have been working on a couple of astropy pull requests, and I would like
> to take advantage of various development tools, but I can't find any
> instructions and they don't seem to do the right thing by default.
>
> * How do I run flake8 to see if my files meet the coding standards? If I
> just run flake8 from the root directory I am submerged in a blizzard of
> warnings from files I have never touched. The same is true of python
> setup.py flake8. I see that there is a CI run that runs flake8 with all
> sorts of warnings turned off, but it's arranged through an environment
> variable so there's no easy way for me to use that (should I?). I can run
> flake8-diff, but again it complains about all sorts of things - often lines
> that are too long - that are clearly acceptable in astropy source code. Is
> the current situation because there are two levels of flake8 compliance -
> one that is needed to allow building at all, and a better one new code
> should meet?
>

This is a great question and I look forward to hearing the answer from one
of our infrastructure gurus.


>
> * How do I clear out the test environment? I find with python setup.py
> test astropy keeps running tests left over from another branch. I have no
> idea where these are stored, perhaps in the virtualenv of the installed
> package?
>

I use the following hammer.  There might be a better way, but I have had
exactly the problem you described and this should fix it.  First:

  $ git clean -nxd  # Check files that are going to be cleaned

Then:

  $ git clean -fxd  # Remove *everything* that is not a tracked git file

Another possibility (maybe try first?) is just `rm -rf build`.  For
instance the `git clean -fxd` will wipe out any IDE settings or other
personal things you might have in the repo.

- Tom


>
> I am happy to add the correct instructions to CONTRIBUTING.rst, when I
> find out what they are.
>
> Thanks,
> Anne
> _______________________________________________
> AstroPy mailing list
> AstroPy at python.org
> https://mail.python.org/mailman/listinfo/astropy
>
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From nathan.goldbaum at gmail.com  Wed Sep 18 14:08:26 2019
From: nathan.goldbaum at gmail.com (Nathan)
Date: Wed, 18 Sep 2019 12:08:26 -0600
Subject: [AstroPy] Instructions for using dev tools
In-Reply-To: <CAMtEP6zcGaNFSu33e5OOX855V7m05BCXwvN6CM0++VdtTZkj3w@mail.gmail.com>
References: <CANm_+Zo2e4Zo+G-0aKTdY1_Tg0w_iCdhF4rD7jNgXZeVRtZvLw@mail.gmail.com>
 <CAMtEP6zcGaNFSu33e5OOX855V7m05BCXwvN6CM0++VdtTZkj3w@mail.gmail.com>
Message-ID: <CAJXewOkT+epC-Mm_W8WWSVmAuGc6ruso_KvXUYrGHv72gR0ACA@mail.gmail.com>

If astropy isn't doing it already, you could probably have the flake8
configuration in a setup.cfg file. Here's what I do for unyt:

https://github.com/yt-project/unyt/blob/master/setup.cfg#L41

With this users just need to run `flake8` in the root of the project and it
"just works".

On Wed, Sep 18, 2019 at 12:06 PM Aldcroft, Thomas <
aldcroft at head.cfa.harvard.edu> wrote:

>
>
> On Wed, Sep 18, 2019 at 12:42 PM Anne Archibald <peridot.faceted at gmail.com>
> wrote:
>
>> Hi,
>>
>> I have been working on a couple of astropy pull requests, and I would
>> like to take advantage of various development tools, but I can't find any
>> instructions and they don't seem to do the right thing by default.
>>
>> * How do I run flake8 to see if my files meet the coding standards? If I
>> just run flake8 from the root directory I am submerged in a blizzard of
>> warnings from files I have never touched. The same is true of python
>> setup.py flake8. I see that there is a CI run that runs flake8 with all
>> sorts of warnings turned off, but it's arranged through an environment
>> variable so there's no easy way for me to use that (should I?). I can run
>> flake8-diff, but again it complains about all sorts of things - often lines
>> that are too long - that are clearly acceptable in astropy source code. Is
>> the current situation because there are two levels of flake8 compliance -
>> one that is needed to allow building at all, and a better one new code
>> should meet?
>>
>
> This is a great question and I look forward to hearing the answer from one
> of our infrastructure gurus.
>
>
>>
>> * How do I clear out the test environment? I find with python setup.py
>> test astropy keeps running tests left over from another branch. I have no
>> idea where these are stored, perhaps in the virtualenv of the installed
>> package?
>>
>
> I use the following hammer.  There might be a better way, but I have had
> exactly the problem you described and this should fix it.  First:
>
>   $ git clean -nxd  # Check files that are going to be cleaned
>
> Then:
>
>   $ git clean -fxd  # Remove *everything* that is not a tracked git file
>
> Another possibility (maybe try first?) is just `rm -rf build`.  For
> instance the `git clean -fxd` will wipe out any IDE settings or other
> personal things you might have in the repo.
>
> - Tom
>
>
>>
>> I am happy to add the correct instructions to CONTRIBUTING.rst, when I
>> find out what they are.
>>
>> Thanks,
>> Anne
>> _______________________________________________
>> 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 p3y1i4n at gmail.com  Mon Sep 23 12:44:54 2019
From: p3y1i4n at gmail.com (Pey Lian Lim)
Date: Mon, 23 Sep 2019 12:44:54 -0400
Subject: [AstroPy] Astropy developer telecon (Sep 2019)
Message-ID: <CAJt49iQQh90xBgRBMA6qBTrCLwE3zbSz=ZOD6bSRW971Wgbrew@mail.gmail.com>

Hello astropy core developers and stakeholders,

You are cordially invited to our September 2019 developer telecon,
mainly to discuss the upcoming 4.0 release
(https://github.com/astropy/astropy/milestones/v4.0). Meeting info as
follows.

Sincerely,
Pey-Lian (on behalf of the Astropy Project)

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

Astropy Project is inviting you to a scheduled Zoom meeting.

Topic: Astropy developer telecon

Time: Sep 24, 2019 02:00 PM Eastern Time (US and Canada)

Join Zoom Meeting

https://zoom.us/j/364224322

One tap mobile
+16468769923,,364224322# US (New York)
+16699006833,,364224322# US (San Jose)

Dial by your location
       +1 646 876 9923 US (New York)
       +1 669 900 6833 US (San Jose)

Meeting ID: 364 224 322

Find your local number: https://zoom.us/u/acK4MK6Tk4

From bsipocz at gmail.com  Mon Sep 23 13:10:55 2019
From: bsipocz at gmail.com (Brigitta Sipocz)
Date: Mon, 23 Sep 2019 10:10:55 -0700
Subject: [AstroPy] ANN: astroquery release v0.3.10
Message-ID: <CAEjJ3fjCaBtx8wQgLsRs4cwnSqdrc03TkSR8A7kcUspNwS_yRg@mail.gmail.com>

Dear All,

We are happy to announce that a new astroquery version, v0.3.10 has been
released and is available both to pip, or conda install (via the astropy or
conda-forge channels).

In this release there are several new services added, as well as numerous
fixes have been made.

Some new additions:
 - module for astrometry.net
 - module for the Canadian Astronomy Data Centre
 - module for the ESA Hubble Archive
 - module IMCCE to access their Miriade and SkyBoT services
 - MAST access to PanSTARRS catalogue data

For a full list, please see the changelog:
https://github.com/astropy/astroquery/blob/v0.3.10/CHANGES.rst

As we did in the past year, we keep continuously releasing developer
versions to PyPI. These can be pip installed with the `--pre` option.

Thank you for everyone who contributed for these releases!

Best wishes,
 Brigitta Sip?cz
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From pdzwig at summaventures.com  Tue Sep 24 05:00:43 2019
From: pdzwig at summaventures.com (Peter Dzwig)
Date: Tue, 24 Sep 2019 10:00:43 +0100
Subject: [AstroPy] Issue when comparing thresholding and derivative changess
 for line-finding
Message-ID: <758a7d89-bd9b-5099-f5c5-e7caa5692f27@summaventures.com>

All,

I am looking at some SDSS spectra, and will ultimately want to identify
individual lines and want to compare thresholding and derivative changes
as techniques to use.

It keeps throwing errors that I can't make head or tail of. The core of
the code is:

["norm_spec" is the continuum normalised spectrum (normalised over the
whole range) which has been transformed to the rest frame.]


    from specutils import SpectralRegion
    from specutils.manipulation import noise_region_uncertainty
    from specutils.fitting import find_lines_threshold,
find_lines_derivative

    noise_region = SpectralRegion(3250*u.AA, 3800*u.AA)
    spec_em_nr=noise_region_uncertainty(norm_spec, noise_region)

# First use thresholding to get lines

    print( '\n'*2,"THRESHOLDING", '\n'*2)
    lines = find_lines_threshold(spec_em_nr, noise_factor=2)

    lem = lines[lines['line_type'] == 'emission']
    labs = lines[lines['line_type'] == 'absorption']

    print("Emission lines (thresholding)",lem[:])

    print("Absorption lines (thresholding)",labs[:])

# Next use derivative to get lines

    print( '\n'*2,"DERIVATIVE", '\n'*2)


    lines = find_lines_derivative(spec_em_nr, flux_threshold=4.0)

    lem2 = lines[lines['line_type'] == 'emission']
    labs2 = lines[lines['line_type'] == 'absorption']

    print("Emission lines (derivative)",lem2[:])

    print("Absorption lines (derivative)",labs2[:])




THRESHOLDING


Emission lines (thresholding)

line_center    line_type line_center_index
   Angstrom
----------------- --------- -----------------
2731.765380859375  emission              1652
2803.130615234375  emission              1764
   4388.775390625  emission              3711

Absorption lines (thresholding) line_center line_type line_center_index
  Angstrom
----------- --------- -----------------


[ Don't expect any ALs. this is just there for completeness]

 DERIVATIVE


Then:

/home/peter/anaconda3/lib/python3.6/site-packages/astropy/table/column.py:965:
FutureWarning: elementwise comparison failed; returning scalar instead,
but in the future will perform elementwise comparison
  return getattr(self.data, op)(other)

---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
<ipython-input-11-2fbc9eae66cc> in <module>()
    288     lines = find_lines_derivative(spec_em_nr, flux_threshold=4.0)
    289
--> 290     lem2 = lines[lines['line_type'] == 'emission']
    291     labs2 = lines[lines['line_type'] == 'absorption']
    292

~/anaconda3/lib/python3.6/site-packages/astropy/table/table.py in
__getitem__(self, item)
   1225             return self.columns[item]
   1226         elif isinstance(item, (int, np.integer)):
-> 1227             return self.Row(self, item)
   1228         elif (isinstance(item, np.ndarray) and item.shape == ()
and item.dtype.kind == 'i'):
   1229             return self.Row(self, item.item())

~/anaconda3/lib/python3.6/site-packages/astropy/table/row.py in
__init__(self, table, index)
     36         if index < -n or index >= n:
     37             raise IndexError('index {0} out of range for table
with length {1}'
---> 38                              .format(index, len(table)))
     39
     40         # Ensure that the row index is positive [#8422]

IndexError: index False out of range for table with length 0


?The thresholding produces results, although poor.

I don't understand the message when doing the derivative, nor why it has
been thrown.

Most of the code comes pretty much straight from the relevant pages in
SpecUtils

Can anyone offer any thoughts? recommendations?

I am running astropy in Jupyter Notebooks, current versions of both and
Ubuntu 18.04 with updates to date.


Peter Dzwig


PS FWIW the spectrum itself is at

<https://data.sdss.org/sas/dr15/sdss/spectro/redux/26/spectra/lite/2107/spec-2107-53786-0069.fits>
-- 

Dr. Peter Dzwig