From hessman at astro.physik.uni-goettingen.de  Wed Aug 14 10:47:19 2019
From: hessman at astro.physik.uni-goettingen.de (Frederic V. Hessman)
Date: Wed, 14 Aug 2019 16:47:19 +0200
Subject: [AstroPy] BCE Time & Dates?
Message-ID: <888A0790-0AA9-4455-AE06-72E4195B0E7C@astro.physik.uni-goettingen.de>

I'm simulating Kepler's "Harmony of the Spheres" using the extended JPL ephemerides not usually available so that I can go back to Bischop Ussher's and Kepler's creation dates, thereby using astropy.time.Time for convenience functions.  However, although

	>>> from astropy.time import Time
	>>> t = Time('4444-10-03T09:00:00')
	>>> str(t)
	'4444-10-03T09:00:00.000'
	>>> t.jd
	3344473.875

obviously works, this doesn't:

	>>> t = Time('-4444-10-03T09:00:00')
	Traceback (most recent call last):
	  File "<stdin>", line 1, in <module>
	  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/astropy/time/core.py", line 399, in __init__
	    precision, in_subfmt, out_subfmt)
	  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/astropy/time/core.py", line 454, in _init_from_vals
	    precision, in_subfmt, out_subfmt)
	  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/astropy/time/core.py", line 505, in _get_time_fmt
	    raise ValueError('Input values did not match {0}'.format(err_msg))
	ValueError: Input values did not match any of the formats where the format keyword is optional ['datetime', 'iso', 'isot', 'yday', 'datetime64', 'fits', 	'byear_str', 'jyear_str']

nor does this:

	>>> t = Time(259237.875,format='jd')
	>>> t.datetime
	Traceback (most recent call last):
	  File "<stdin>", line 1, in <module>
	  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/astropy/time/core.py", line 1542, in __getattr__
	    value = tm._shaped_like_input(tm._time.to_value(parent=tm))
	  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/astropy/time/formats.py", line 682, in to_value
	    out[...] = datetime.datetime(iy, im, id, ihr, imin, isec, ifracsec)
	ValueError: year is out of range

and other attempts simply return garbage along with the message

	WARNING: ErfaWarning: ERFA function "d2dtf" yielded 1 of "dubious year (Note 5)" [astropy._erfa.core]

Why is a BCE date garbagge or "dubious"?

Rick


From derek at astro.physik.uni-goettingen.de  Wed Aug 14 13:30:05 2019
From: derek at astro.physik.uni-goettingen.de (Derek Homeier)
Date: Wed, 14 Aug 2019 19:30:05 +0200
Subject: [AstroPy] BCE Time & Dates?
In-Reply-To: <888A0790-0AA9-4455-AE06-72E4195B0E7C@astro.physik.uni-goettingen.de>
References: <888A0790-0AA9-4455-AE06-72E4195B0E7C@astro.physik.uni-goettingen.de>
Message-ID: <E1D074C7-CB9F-4182-BFAE-F00A5488B2A1@astro.physik.uni-goettingen.de>

Hi Rick,
> 
> I'm simulating Kepler's "Harmony of the Spheres" using the extended JPL ephemerides not usually available so that I can go back to Bischop Ussher's and Kepler's creation dates, thereby using astropy.time.Time for convenience functions.  However, although
> 
> 	>>> from astropy.time import Time
> 	>>> t = Time('4444-10-03T09:00:00')
> 	>>> str(t)
> 	'4444-10-03T09:00:00.000'
> 	>>> t.jd
> 	3344473.875
> 
> obviously works, this doesn?t:
> 
maybe the Bishop was right? ;-)

> 	>>> t = Time('-4444-10-03T09:00:00')
> 	Traceback (most recent call last):

`Time` does support a class of `long*` subformats, which are even automatically recognised,
but somewhat less than intuitive - they require a sign+5-digit year format!

 t = Time(?-04444-10-03T09:00:00?)

should work (at least create a valid Time object. Not sure if there is a logical reason why
signed 4-digit years cannot be recognised (other than apparently only exactly two year
formats being defined; so <4 digits are not accepted either). Might be worth filing an issue.

The `datetime` overflow is a limitation of the builtin library:
datetime.MINYEAR
The smallest year number allowed in a date or datetime object. MINYEAR is 1.

so nothing you can really do about it at the Astropy level.

HTH
					Derek


From derek at astro.physik.uni-goettingen.de  Wed Aug 14 13:53:32 2019
From: derek at astro.physik.uni-goettingen.de (Derek Homeier)
Date: Wed, 14 Aug 2019 19:53:32 +0200
Subject: [AstroPy] BCE Time & Dates?
In-Reply-To: <E1D074C7-CB9F-4182-BFAE-F00A5488B2A1@astro.physik.uni-goettingen.de>
References: <888A0790-0AA9-4455-AE06-72E4195B0E7C@astro.physik.uni-goettingen.de>
 <E1D074C7-CB9F-4182-BFAE-F00A5488B2A1@astro.physik.uni-goettingen.de>
Message-ID: <8B49902F-2F01-4100-83A5-4FAE08E6F2AE@astro.physik.uni-goettingen.de>

On 14 Aug 2019, at 7:30 pm, Derek Homeier <derek at astro.physik.uni-goettingen.de> wrote:
> 
>> 	>>> t = Time('-4444-10-03T09:00:00')
>> 	Traceback (most recent call last):
> 
> `Time` does support a class of `long*` subformats, which are even automatically recognised,
> but somewhat less than intuitive - they require a sign+5-digit year format!
> 
> t = Time(?-04444-10-03T09:00:00?)
> 
> should work (at least create a valid Time object. Not sure if there is a logical reason why
> signed 4-digit years cannot be recognised (other than apparently only exactly two year
> formats being defined; so <4 digits are not accepted either). Might be worth filing an issue.

Possibility some justification (as well as discussion of the existence of a ?year 0? - i.e.
?-04444? is the year 4445 BC!) is found in the corresponding FITS paper:
https://www.aanda.org/articles/aa/abs/2015/02/aa24653-14/aa24653-14.html

Cheers,
					Derek


From leonardo.parisi at gmail.com  Thu Aug 15 05:25:21 2019
From: leonardo.parisi at gmail.com (Leonardo Parisi)
Date: Thu, 15 Aug 2019 11:25:21 +0200
Subject: [AstroPy] From pixels to RA DEC
Message-ID: <CAMNDLnk8800hVSh8GO_0S-LGmTo4Z=UbCAdupUUef0D_yJRXxA@mail.gmail.com>

Hi,

I'm looking to the formula used by Astropy to convert from pixels to ra/dec

After take care of distortions the formula used is this?

[image: Screenshot 2019-08-15 at 10.46.28.png]

where RA0 and DEC0 are the coordinates of the center of the image
gamma the pixel scale and alpha the rotational angle
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From gordon.b.dennis at gmail.com  Sat Aug 17 11:11:03 2019
From: gordon.b.dennis at gmail.com (Gordon Dennis)
Date: Sat, 17 Aug 2019 16:11:03 +0100
Subject: [AstroPy] Problem querying NED with astropy
Message-ID: <000d01d5550d$fd530570$f7f91050$@gmail.com>

Good morning

I want to use astropy on Windows 10 to query the NASA extragalactic database
(NED), but I'm having a very frustrating time getting even the simplest
things to work..

1.       Installed Python36.

2.       Tried pip install astropy.  
Result - fatal error.

3.       Tried 2 more times
Same result.

4.       I read that if you install Python36 using the Anaconda
distribution, astropy is included, so:

5.       I de-installed Python36 and .

6.       . installed Anaconda 

7.       Ran the Spyder IDE (Spyder is loaded automatically with Anaconda),
and tried this very simple code (it's actually an example I copied from the
www.astropy.org , apart from the argument 'NGC 1300' which is one of the
galaxies I'm studying):

from astroquery.ned import Ned

result_table = Ned.query_object("NGC 1300")

print(result_table) # an astropy.table.Table

Now you get the error message 'unable to import Ned'.  So, I guess it's
seeing astropy but failing to recognize Ned.  Obviously line 2 & 3 don't get
executed.  If I run the line 
from astroquery.ned import Ned in a windows command box and execute with
Python36 I get the same result.

8.       I assume (since the example above was copied from the astropy web
site that 'Ned' with the uppercase 'N' is correct.  I'm now 7 hours down and
beginning to loose hope.  What am I doing wrong/have missed or whatever?

Would greatly appreciate any steers you can give me.

Gordon Dennis

p.s. yes I do have admin privileges; and my Windows 10 is fully updated.

 

 

+44(0)1934 838096 / +44(0)7774628110 / Skype: gordon.dennis

Sent from my Analytical Engine

Description: analyticalEngine

 

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From shupe at ipac.caltech.edu  Sun Aug 18 11:18:37 2019
From: shupe at ipac.caltech.edu (Shupe, David L.)
Date: Sun, 18 Aug 2019 15:18:37 +0000
Subject: [AstroPy] Problem querying NED with astropy
In-Reply-To: <000d01d5550d$fd530570$f7f91050$@gmail.com>
References: <000d01d5550d$fd530570$f7f91050$@gmail.com>
Message-ID: <B0FD20C0-C98C-46BF-89E5-D2D6230F968B@caltech.edu>

Hello Gordon,

Thank you for your inquiry about using astroquery.ned. The astroquery package is not included with Anaconda, so there is an additional installation needed for it.

Following https://astroquery.readthedocs.io/en/latest/, since you have Anaconda installed, you can do ?conda install -c astropy astroquery? to get a tagged release. Or, for the latest version you can instead do ?pip install --pre astroquery?.

Please feel free to contact me off-list if you have further questions, or are otherwise having trouble with the module for NED.

Regards,
David Shupe
Caltech/IPAC

On Aug 17, 2019, at 8:11 AM, Gordon Dennis <gordon.b.dennis at gmail.com<mailto:gordon.b.dennis at gmail.com>> wrote:

Good morning
I want to use astropy on Windows 10 to query the NASA extragalactic database (NED), but I'm having a very frustrating time getting even the simplest things to work..

1.       Installed Python36.

2.       Tried pip install astropy.
Result - fatal error.

3.       Tried 2 more times
Same result.

4.       I read that if you install Python36 using the Anaconda distribution, astropy is included, so:

5.       I de-installed Python36 and ?

6.       ? installed Anaconda

7.       Ran the Spyder IDE (Spyder is loaded automatically with Anaconda), and tried this very simple code (it's actually an example I copied from the www.astropy.org<http://www.astropy.org/> , apart from the argument ?NGC 1300? which is one of the galaxies I?m studying):

from astroquery.ned import Ned
result_table = Ned.query_object("NGC 1300")
print(result_table) # an astropy.table.Table
Now you get the error message 'unable to import Ned'.  So, I guess it?s seeing astropy but failing to recognize Ned.  Obviously line 2 & 3 don?t get executed.  If I run the line
from astroquery.ned import Ned in a windows command box and execute with Python36 I get the same result.

8.       I assume (since the example above was copied from the astropy web site that ?Ned? with the uppercase ?N? is correct.  I'm now 7 hours down and beginning to loose hope.  What am I doing wrong/have missed or whatever?
Would greatly appreciate any steers you can give me.
Gordon Dennis
p.s. yes I do have admin privileges; and my Windows 10 is fully updated.


+44(0)1934 838096 / +44(0)7774628110 / Skype: gordon.dennis
Sent from my Analytical Engine
<image003.jpg>

_______________________________________________
AstroPy mailing list
AstroPy at python.org<mailto:AstroPy at python.org>
https://mail.python.org/mailman/listinfo/astropy

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From antigone.lambert-huyghe at cea.fr  Fri Aug 23 08:10:17 2019
From: antigone.lambert-huyghe at cea.fr (LAMBERT-HUYGHE Antigone)
Date: Fri, 23 Aug 2019 12:10:17 +0000
Subject: [AstroPy] Problem with the latest version of astropy and numpy
Message-ID: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312AFCC@e-exdage-b0.extra.cea.fr>

Hi everyone,

I post here because I don't really know where to advise of that problem.

I use a convolution function from astropy.convolution package. I call it with

result = [astropy.convolution.]convolve(inhdu[0].data, kernel, boundary = 'fill', fill_value = float('NaN'), preserve_nan=True)

where inhdu[0].data is a numpy array, type float32, and a size of ~24000x25000 pixels, and where kernel is a gaussian kernel created with [astropy.convolution.]Gaussian2DKernel.

I previously had version 3.1.X of astropy, and 1.16.X of numpy, and the convolution was working fine. But the packages went to versions 3.2 on mid-june and 1.17 at the end of july respectively, and I have now an error with the upgraded packages:



~/Bureau/Codes/python_lib/mylib/fits.py in fits_convolve(infits, fromfwhm, tofwhm, GaussianTrim, WriteTo, pixkey, pixkey_unit, returnHDU, verbose)
    640             result[i, :, :] = convolve(plane, kernel, boundary = 'fill', fill_value = float('NaN'), preserve_nan=True)
    641     else:
--> 642         result = convolve(inhdu[0].data, kernel, boundary = 'fill', fill_value = float('NaN'), preserve_nan=True)
    643         #result = convolve_fft(inhdu[0].data, kernel)
    644

~/.local/lib/python3.6/site-packages/astropy/nddata/decorators.py in wrapper(data, *args, **kwargs)
    244                                   AstropyUserWarning)
    245
--> 246             result = func(data, *args, **kwargs)
    247
    248             if unpack and repack:

~/.local/lib/python3.6/site-packages/astropy/convolution/convolve.py in convolve(array, kernel, boundary, fill_value, nan_treatment, normalize_kernel, mask, preserve_nan, normalization_zero_tol)
    336     if normalize_kernel:
    337         if not nan_interpolate:
--> 338             result /= kernel_sum
    339     else:
    340         if nan_interpolate:

~/.local/lib/python3.6/site-packages/astropy/units/quantity.py in __array_ufunc__(self, function, method, *inputs, **kwargs)
    473             return result
    474
--> 475         return self._result_as_quantity(result, unit, out)
    476
    477     def _result_as_quantity(self, result, unit, out):

~/.local/lib/python3.6/site-packages/astropy/units/quantity.py in _result_as_quantity(self, result, unit, out)
    512         # the output is of the correct Quantity subclass, as it was passed
    513         # through check_output.
--> 514         out._set_unit(unit)
    515         return out
    516

AttributeError: 'numpy.ndarray' object has no attribute '_set_unit'


I tried to understand the problem, but I'm stuck and I really need that function to work. For the moment I will just reinstall previous versions for both packages, because it was working before the upgrade, but I wanted to let it know if it is a bug due to latest versions. It may be not in astropy package but in numpy package, but I was not able to understand that too.

I hope this message is not too long, but I wanted to make it as clear as possible.

Best regards

Antigone Lambert-Huyghe
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From kanderso at gemini.edu  Fri Aug 23 11:04:23 2019
From: kanderso at gemini.edu (Kenneth Anderson)
Date: Fri, 23 Aug 2019 11:04:23 -0400
Subject: [AstroPy] Problem with the latest version of astropy and numpy
In-Reply-To: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312AFCC@e-exdage-b0.extra.cea.fr>
References: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312AFCC@e-exdage-b0.extra.cea.fr>
Message-ID: <CAAye0vs=maUhykP=4W1JpW1k+es4OcYkHW2CfL+QpzyxPk1BqA@mail.gmail.com>

Hi Antigone,

I cannot be sure how this problem arises for you, but what can be said is
that an AttributeError thrown from the numpy object is way off base for
that function. According the docstr on the* _result_as_quantity()*, the
return object, i.e. the  *'out'* object, should be an
*astropy.units.Quantity* object, not a *numpy* object.

It is unclear where things got confused in the call stack: perhaps an
incorrect object type was passed initially? You may want to *absolutely
ensure* that this did work under the previous versions. And if so, then it
would seem something is amiss in that astropy call stack.

>From the docstr:
---------------------
*_result_as_quantity(self, result, unit, out):

    *
*        [ ... ]
                                                                *
*        Parameters

           *
*        ----------

           *
*        result : *`~numpy.ndarray` or tuple of `~numpy.ndarray`


            Array(s) which need to be turned into quantity.


*        unit : `~astropy.units.Unit` or None

           *
            Unit for the quantities to be returned (or `None` if the result


            should not be a quantity).  Should be tuple if result is a
tuple.

*        out : `~astropy.units.Quantity` or None

            *
            Possible output quantity. Should be `None` or a tuple if result


            is a tuple.





*        Returns

            *
*        -------

            *
*        out : `~astropy.units.Quantity`

            *
*           With units set.*

salud,
k
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From rowen at uw.edu  Fri Aug 23 18:37:49 2019
From: rowen at uw.edu (Russell Owen)
Date: Fri, 23 Aug 2019 15:37:49 -0700
Subject: [AstroPy] How to compute TAI-UTC using Astropy?
In-Reply-To: <CAAye0vs=maUhykP=4W1JpW1k+es4OcYkHW2CfL+QpzyxPk1BqA@mail.gmail.com>
References: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312AFCC@e-exdage-b0.extra.cea.fr>
 <CAAye0vs=maUhykP=4W1JpW1k+es4OcYkHW2CfL+QpzyxPk1BqA@mail.gmail.com>
Message-ID: <2B2DEF60-49E8-4F54-AF54-CF3951DE88EC@uw.edu>

We do some work with TAI times as unix seconds. Possibly controversial, but it?s what we use.

We sometimes need to convert normal unix times (UTC) to this standard.

This naive solution does not work:

def bogus_tai_from_utc(utc):
    ???Failed attempt to return TAI in unix seconds given UTC in unix seconds.
  
    This fails because given an astropy.time.Time astropy_time:
    astropy_time.tai.unix == astropy_time.utc.unix
    """
    return astropy.time.Time(utc, format=?unix?, scale=?utc?).tai.unix

Is there a nice way to ask AstroPy the value of TAI-UTC in seconds, given a UTC?
If so, this would be perfect:

tai_from_utc(utc):
    tai_minus_utc = ?? (presently 37 seconds)
    return utc + tai_minus_utc

The following ugly code works, but has error at the microsecond level and may not work at leap seconds:

tai_minus_utc = (astropy_utc.tai.mjd - astropy_utc.utc.mjd)*24*60*60 

Regards,

Russell

From npross at roe.ac.uk  Sat Aug 24 07:06:34 2019
From: npross at roe.ac.uk (Nicholas Ross)
Date: Sat, 24 Aug 2019 11:06:34 +0000
Subject: [AstroPy] Weird Pyraf issues
In-Reply-To: <mailman.182.1566572676.30343.astropy@python.org>
References: <mailman.182.1566572676.30343.astropy@python.org>
Message-ID: <6F23E02E-BA76-4332-8E10-24B8979C421F@roe.ac.uk>

Hi there, 

I am having big difficulties with my Pyraf install, namely, my whole MacBook Pro (OS X 10.14.6) 
crashes whenever I try and simply open an IRAF graphics window, e.g. 

> source activate iraf27
	(iraf27) ~/DataReduction/20190628 > ipython
	Python 2.7.16 |Anaconda, Inc.| (default, Aug 22 2019, 10:59:10) 
	Type "copyright", "credits" or "license" for more information.
	IPython 5.8.0 -- An enhanced Interactive Python.
	?         -> Introduction and overview of IPython's features.
	%quickref -> Quick reference.
	help      -> Python's own help system.
	object?   -> Details about 'object', use 'object??' for extra details.
	Using matplotlib backend: TkAgg

	In [1]: from pyraf import iraf

	In [2]: iraf.splot('r2824072.fit[1]?)

From here, I get directly booted out and back to the Mac login screen (yup, seriously!) 

I?ve just re-installed the conda distribution from 
https://astroconda.readthedocs.io/en/latest/updating.html#updating-conda
> conda create -n iraf27 python=2.7 iraf-all pyraf-all stsci

However, if I start an xgterm, and then do 
> cl 
and run IRAF from that command line, I can then do splot fine. 

Any help would be *SO* appreciated!!

Yours, 
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 zff1991 at mail.ustc.edu.cn  Sat Aug 24 09:41:29 2019
From: zff1991 at mail.ustc.edu.cn (Zhu Fei-Fan)
Date: Sat, 24 Aug 2019 09:41:29 -0400
Subject: [AstroPy] Weird Pyraf issues
In-Reply-To: <6F23E02E-BA76-4332-8E10-24B8979C421F@roe.ac.uk>
References: <mailman.182.1566572676.30343.astropy@python.org>
 <6F23E02E-BA76-4332-8E10-24B8979C421F@roe.ac.uk>
Message-ID: <CAPTcXymWfuktf=bSUANeDHqyRy=s=QpXyN70kkP_yXh4DoUp9Q@mail.gmail.com>

The recent version of DS9 (mac) also suffer from the very same issue under
OS X 10.14.6.


On Sat, 24 Aug 2019 at 08:00, Nicholas Ross <npross at roe.ac.uk> wrote:

> Hi there,
>
> I am having big difficulties with my Pyraf install, namely, my whole
> MacBook Pro (OS X 10.14.6)
> crashes whenever I try and simply open an IRAF graphics window, e.g.
>
> > source activate iraf27
>         (iraf27) ~/DataReduction/20190628 > ipython
>         Python 2.7.16 |Anaconda, Inc.| (default, Aug 22 2019, 10:59:10)
>         Type "copyright", "credits" or "license" for more information.
>         IPython 5.8.0 -- An enhanced Interactive Python.
>         ?         -> Introduction and overview of IPython's features.
>         %quickref -> Quick reference.
>         help      -> Python's own help system.
>         object?   -> Details about 'object', use 'object??' for extra
> details.
>         Using matplotlib backend: TkAgg
>
>         In [1]: from pyraf import iraf
>
>         In [2]: iraf.splot('r2824072.fit[1]?)
>
> From here, I get directly booted out and back to the Mac login screen
> (yup, seriously!)
>
> I?ve just re-installed the conda distribution from
> https://astroconda.readthedocs.io/en/latest/updating.html#updating-conda
> > conda create -n iraf27 python=2.7 iraf-all pyraf-all stsci
>
> However, if I start an xgterm, and then do
> > cl
> and run IRAF from that command line, I can then do splot fine.
>
> Any help would be *SO* appreciated!!
>
> Yours,
> 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
>
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From aldcroft at head.cfa.harvard.edu  Sat Aug 24 17:12:16 2019
From: aldcroft at head.cfa.harvard.edu (Aldcroft, Thomas)
Date: Sat, 24 Aug 2019 17:12:16 -0400
Subject: [AstroPy] How to compute TAI-UTC using Astropy?
In-Reply-To: <2B2DEF60-49E8-4F54-AF54-CF3951DE88EC@uw.edu>
References: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312AFCC@e-exdage-b0.extra.cea.fr>
 <CAAye0vs=maUhykP=4W1JpW1k+es4OcYkHW2CfL+QpzyxPk1BqA@mail.gmail.com>
 <2B2DEF60-49E8-4F54-AF54-CF3951DE88EC@uw.edu>
Message-ID: <CAMtEP6zUmGEVoAaX+sMq07_xtLxZ6XTXsCOZZVhbh5Lrj7-mYw@mail.gmail.com>

Hi Russell,

I think what you want is:

In [1]: from astropy.time import Time
In [2]: date = '2019-08-24 00:00:00'
In [3]: dt = Time(date, scale='utc') - Time(date, scale='tai')
In [4]: dt.sec
Out[4]: 36.99999999999779

- Tom

On Fri, Aug 23, 2019 at 6:46 PM Russell Owen <rowen at uw.edu> wrote:

> We do some work with TAI times as unix seconds. Possibly controversial,
> but it?s what we use.
>
> We sometimes need to convert normal unix times (UTC) to this standard.
>
> This naive solution does not work:
>
> def bogus_tai_from_utc(utc):
>     ???Failed attempt to return TAI in unix seconds given UTC in unix
> seconds.
>
>     This fails because given an astropy.time.Time astropy_time:
>     astropy_time.tai.unix == astropy_time.utc.unix
>     """
>     return astropy.time.Time(utc, format=?unix?, scale=?utc?).tai.unix
>
> Is there a nice way to ask AstroPy the value of TAI-UTC in seconds, given
> a UTC?
> If so, this would be perfect:
>
> tai_from_utc(utc):
>     tai_minus_utc = ?? (presently 37 seconds)
>     return utc + tai_minus_utc
>
> The following ugly code works, but has error at the microsecond level and
> may not work at leap seconds:
>
> tai_minus_utc = (astropy_utc.tai.mjd - astropy_utc.utc.mjd)*24*60*60
>
> Regards,
>
> Russell
> _______________________________________________
> AstroPy mailing list
> AstroPy at python.org
> https://mail.python.org/mailman/listinfo/astropy
>
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From rowen at uw.edu  Sat Aug 24 19:24:26 2019
From: rowen at uw.edu (Russell Owen)
Date: Sat, 24 Aug 2019 16:24:26 -0700
Subject: [AstroPy] How to compute TAI-UTC using Astropy?
In-Reply-To: <CAMtEP6zUmGEVoAaX+sMq07_xtLxZ6XTXsCOZZVhbh5Lrj7-mYw@mail.gmail.com>
References: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312AFCC@e-exdage-b0.extra.cea.fr>
 <CAAye0vs=maUhykP=4W1JpW1k+es4OcYkHW2CfL+QpzyxPk1BqA@mail.gmail.com>
 <2B2DEF60-49E8-4F54-AF54-CF3951DE88EC@uw.edu>
 <CAMtEP6zUmGEVoAaX+sMq07_xtLxZ6XTXsCOZZVhbh5Lrj7-mYw@mail.gmail.com>
Message-ID: <665327DD-816A-41AA-BFC0-33D5AB975B3E@uw.edu>

Thank you for the suggestion, but I?m afraid I don?t see how it works.. The given date I have to work from is a date in UTC. By specifying ?Time(date, scale=?tai?)? I would be lying to the system: saying the date was TAI when it is UTC. I would expect that to give the wrong answer very near a UTC leap second.

My code didn?t work at leap second either, but this code does:

def tai_from_utc(utc):
    """Return TAI in unix seconds, given UTC in unix seconds.
    """
    astropy_utc = astropy.time.Time(utc, scale="utc", format="unix")
    dt_utc = astropy_utc.utc.to_datetime()
    dt_tai = astropy_utc.tai.to_datetime()
    tai_minus_utc = (dt_tai - dt_utc).total_seconds()
    return utc + tai_minus_utc

It seems quite clumsy to have to use datetime objects *and* astropy. I?d welcome a cleaner solution!

Regards,

Russell

> On Aug 24, 2019, at 2:12 PM, Aldcroft, Thomas <aldcroft at head.cfa.harvard.edu> wrote:
> 
> Hi Russell,
> 
> I think what you want is:
> 
> In [1]: from astropy.time import Time
> In [2]: date = '2019-08-24 00:00:00'
> In [3]: dt = Time(date, scale='utc') - Time(date, scale='tai')
> In [4]: dt.sec
> Out[4]: 36.99999999999779
> 
> - Tom
> 
> On Fri, Aug 23, 2019 at 6:46 PM Russell Owen <rowen at uw.edu <mailto:rowen at uw.edu>> wrote:
> We do some work with TAI times as unix seconds. Possibly controversial, but it?s what we use.
> 
> We sometimes need to convert normal unix times (UTC) to this standard.
> 
> This naive solution does not work:
> 
> def bogus_tai_from_utc(utc):
>     ???Failed attempt to return TAI in unix seconds given UTC in unix seconds.
> 
>     This fails because given an astropy.time.Time astropy_time:
>     astropy_time.tai.unix == astropy_time.utc.unix
>     """
>     return astropy.time.Time(utc, format=?unix?, scale=?utc?).tai.unix
> 
> Is there a nice way to ask AstroPy the value of TAI-UTC in seconds, given a UTC?
> If so, this would be perfect:
> 
> tai_from_utc(utc):
>     tai_minus_utc = ?? (presently 37 seconds)
>     return utc + tai_minus_utc
> 
> The following ugly code works, but has error at the microsecond level and may not work at leap seconds:
> 
> tai_minus_utc = (astropy_utc.tai.mjd - astropy_utc.utc.mjd)*24*60*60 
> 
> Regards,
> 
> Russell
> _______________________________________________
> 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
> https://mail.python.org/mailman/listinfo/astropy

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From aldcroft at head.cfa.harvard.edu  Sun Aug 25 06:42:32 2019
From: aldcroft at head.cfa.harvard.edu (Aldcroft, Thomas)
Date: Sun, 25 Aug 2019 06:42:32 -0400
Subject: [AstroPy] How to compute TAI-UTC using Astropy?
In-Reply-To: <665327DD-816A-41AA-BFC0-33D5AB975B3E@uw.edu>
References: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312AFCC@e-exdage-b0.extra.cea.fr>
 <CAAye0vs=maUhykP=4W1JpW1k+es4OcYkHW2CfL+QpzyxPk1BqA@mail.gmail.com>
 <2B2DEF60-49E8-4F54-AF54-CF3951DE88EC@uw.edu>
 <CAMtEP6zUmGEVoAaX+sMq07_xtLxZ6XTXsCOZZVhbh5Lrj7-mYw@mail.gmail.com>
 <665327DD-816A-41AA-BFC0-33D5AB975B3E@uw.edu>
Message-ID: <CAMtEP6yBp2FUneLH=Nk5gUf4ZVwVvUSqSTkMyLXDvKsFmPhpjw@mail.gmail.com>

On Sat, Aug 24, 2019 at 7:24 PM Russell Owen <rowen at uw.edu> wrote:

> Thank you for the suggestion, but I?m afraid I don?t see how it works..
> The given date I have to work from is a date in UTC. By specifying
> ?Time(date, scale=?tai?)? I would be lying to the system: saying the date
> was TAI when it is UTC. I would expect that to give the wrong answer very
> near a UTC leap second.
>

I think the code works as expected within a leap second, at the expense of
an ERFA warning that you would need to catch:

In [2]: dts = [0, 0.5, 1.0, 1.5, 1.99, 2.0, 2.5, 3.0] * u.s
In [3]: dates_utc = Time(Time('2015-06-30 23:59:59') + dts, scale='utc')
In [4]: dates_tai = Time(dates_utc.iso, scale='tai')
WARNING: ErfaWarning: ERFA function "dtf2d" yielded 3 of "time is after end
of day (Note 5)" [astropy._erfa.core]
In [5]: for date_utc, date_tai in zip(dates_utc, dates_tai):
   ...:     print(f'{date_utc} {(date_utc - date_tai).sec:.2f}')
   ...:
2015-06-30 23:59:59.000 35.00
2015-06-30 23:59:59.500 35.00
2015-06-30 23:59:60.000 35.00
2015-06-30 23:59:60.500 35.00
2015-06-30 23:59:60.990 35.00
2015-07-01 00:00:00.000 36.00
2015-07-01 00:00:00.500 36.00
2015-07-01 00:00:01.000 36.00


>
> My code didn?t work at leap second either, but this code does:
>
> def tai_from_utc(utc):
>     """Return TAI in unix seconds, given UTC in unix seconds.
>     """
>     astropy_utc = astropy.time.Time(utc, scale="utc", format="unix")
>     dt_utc = astropy_utc.utc.to_datetime()
>     dt_tai = astropy_utc.tai.to_datetime()
>     tai_minus_utc = (dt_tai - dt_utc).total_seconds()
>     return utc + tai_minus_utc
>

On this, I would caution against using the astropy unix format for
calculations where the details matter.  From the TimeUnix API docs
<https://docs.astropy.org/en/stable/api/astropy.time.TimeUnix.html#astropy.time.TimeUnix>
:

*NOTE: this quantity is not exactly unix time and differs from the strict
POSIX definition by up to 1 second on days with a leap second. POSIX unix
time actually jumps backward by 1 second at midnight on leap second days
while this class value is monotonically increasing at 86400 seconds per UTC
day.*

I'm not sure about your test case, but the Python `datetime` does not
support leap seconds.  I got this exception trying to run your code within
a leap second, but maybe I did something differently:

ValueError: Time (array(2015, dtype=int32), array(6, dtype=int32),
array(30, dtype=int32), array(23, dtype=int32), array(59, dtype=int32),
array(60, dtype=int32), array(0, dtype=int32)) is within a leap second but
datetime does not support leap seconds

Cheers,
Tom


>
> It seems quite clumsy to have to use datetime objects *and* astropy. I?d
> welcome a cleaner solution!
>
> Regards,
>
> Russell
>
> On Aug 24, 2019, at 2:12 PM, Aldcroft, Thomas <
> aldcroft at head.cfa.harvard.edu> wrote:
>
> Hi Russell,
>
> I think what you want is:
>
> In [1]: from astropy.time import Time
> In [2]: date = '2019-08-24 00:00:00'
> In [3]: dt = Time(date, scale='utc') - Time(date, scale='tai')
> In [4]: dt.sec
> Out[4]: 36.99999999999779
>
> - Tom
>
> On Fri, Aug 23, 2019 at 6:46 PM Russell Owen <rowen at uw.edu> wrote:
>
>> We do some work with TAI times as unix seconds. Possibly controversial,
>> but it?s what we use.
>>
>> We sometimes need to convert normal unix times (UTC) to this standard.
>>
>> This naive solution does not work:
>>
>> def bogus_tai_from_utc(utc):
>>     ???Failed attempt to return TAI in unix seconds given UTC in unix
>> seconds.
>>
>>     This fails because given an astropy.time.Time astropy_time:
>>     astropy_time.tai.unix == astropy_time.utc.unix
>>     """
>>     return astropy.time.Time(utc, format=?unix?, scale=?utc?).tai.unix
>>
>> Is there a nice way to ask AstroPy the value of TAI-UTC in seconds, given
>> a UTC?
>> If so, this would be perfect:
>>
>> tai_from_utc(utc):
>>     tai_minus_utc = ?? (presently 37 seconds)
>>     return utc + tai_minus_utc
>>
>> The following ugly code works, but has error at the microsecond level and
>> may not work at leap seconds:
>>
>> tai_minus_utc = (astropy_utc.tai.mjd - astropy_utc.utc.mjd)*24*60*60
>>
>> Regards,
>>
>> Russell
>> _______________________________________________
>> 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 dburke.gw at gmail.com  Sun Aug 25 09:32:57 2019
From: dburke.gw at gmail.com (Doug Burke)
Date: Sun, 25 Aug 2019 09:32:57 -0400
Subject: [AstroPy] Weird Pyraf issues
In-Reply-To: <CAPTcXymWfuktf=bSUANeDHqyRy=s=QpXyN70kkP_yXh4DoUp9Q@mail.gmail.com>
References: <mailman.182.1566572676.30343.astropy@python.org>
 <6F23E02E-BA76-4332-8E10-24B8979C421F@roe.ac.uk>
 <CAPTcXymWfuktf=bSUANeDHqyRy=s=QpXyN70kkP_yXh4DoUp9Q@mail.gmail.com>
Message-ID: <CALkjVLDNYCdC_N=x+grjuv7AWRRZf+5Uw5ERBq720-J2BKZvvg@mail.gmail.com>

Apple decided to "improve" things in Mojave, which broke DS9. The latest
beta release (8.1b2) should fix this -
https://twitter.com/SAOImageDS9/status/1161031804695896064 - or, for a
more-direct link - see http://ds9.si.edu/site/Beta.html

I don't know if this helps Nic [there was unfortunately no follow up to
Karl's remark at
https://twitter.com/karlglazebrook/status/1161785531551797250 ]

Doug

On Sat, Aug 24, 2019 at 9:42 AM Zhu Fei-Fan <zff1991 at mail.ustc.edu.cn>
wrote:

> The recent version of DS9 (mac) also suffer from the very same issue under
> OS X 10.14.6.
>
>
> On Sat, 24 Aug 2019 at 08:00, Nicholas Ross <npross at roe.ac.uk> wrote:
>
>> Hi there,
>>
>> I am having big difficulties with my Pyraf install, namely, my whole
>> MacBook Pro (OS X 10.14.6)
>> crashes whenever I try and simply open an IRAF graphics window, e.g.
>>
>> > source activate iraf27
>>         (iraf27) ~/DataReduction/20190628 > ipython
>>         Python 2.7.16 |Anaconda, Inc.| (default, Aug 22 2019, 10:59:10)
>>         Type "copyright", "credits" or "license" for more information.
>>         IPython 5.8.0 -- An enhanced Interactive Python.
>>         ?         -> Introduction and overview of IPython's features.
>>         %quickref -> Quick reference.
>>         help      -> Python's own help system.
>>         object?   -> Details about 'object', use 'object??' for extra
>> details.
>>         Using matplotlib backend: TkAgg
>>
>>         In [1]: from pyraf import iraf
>>
>>         In [2]: iraf.splot('r2824072.fit[1]?)
>>
>> From here, I get directly booted out and back to the Mac login screen
>> (yup, seriously!)
>>
>> I?ve just re-installed the conda distribution from
>> https://astroconda.readthedocs.io/en/latest/updating.html#updating-conda
>> > conda create -n iraf27 python=2.7 iraf-all pyraf-all stsci
>>
>> However, if I start an xgterm, and then do
>> > cl
>> and run IRAF from that command line, I can then do splot fine.
>>
>> Any help would be *SO* appreciated!!
>>
>> Yours,
>> 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
>>
> _______________________________________________
> AstroPy mailing list
> AstroPy at python.org
> https://mail.python.org/mailman/listinfo/astropy
>
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From rowen at uw.edu  Sun Aug 25 11:20:16 2019
From: rowen at uw.edu (Russell Owen)
Date: Sun, 25 Aug 2019 08:20:16 -0700
Subject: [AstroPy] How to compute TAI-UTC using Astropy?
In-Reply-To: <CAMtEP6yBp2FUneLH=Nk5gUf4ZVwVvUSqSTkMyLXDvKsFmPhpjw@mail.gmail.com>
References: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312AFCC@e-exdage-b0.extra.cea.fr>
 <CAAye0vs=maUhykP=4W1JpW1k+es4OcYkHW2CfL+QpzyxPk1BqA@mail.gmail.com>
 <2B2DEF60-49E8-4F54-AF54-CF3951DE88EC@uw.edu>
 <CAMtEP6zUmGEVoAaX+sMq07_xtLxZ6XTXsCOZZVhbh5Lrj7-mYw@mail.gmail.com>
 <665327DD-816A-41AA-BFC0-33D5AB975B3E@uw.edu>
 <CAMtEP6yBp2FUneLH=Nk5gUf4ZVwVvUSqSTkMyLXDvKsFmPhpjw@mail.gmail.com>
Message-ID: <A337DB5E-23CA-47B0-8FEB-8ABBED76C701@uw.edu>


> On Aug 25, 2019, at 3:42 AM, Aldcroft, Thomas <aldcroft at head.cfa.harvard.edu> wrote:
> 
> 
> 
> On Sat, Aug 24, 2019 at 7:24 PM Russell Owen <rowen at uw.edu <mailto:rowen at uw.edu>> wrote:
> Thank you for the suggestion, but I?m afraid I don?t see how it works.. The given date I have to work from is a date in UTC. By specifying ?Time(date, scale=?tai?)? I would be lying to the system: saying the date was TAI when it is UTC. I would expect that to give the wrong answer very near a UTC leap second.
> 
> I think the code works as expected within a leap second, at the expense of an ERFA warning that you would need to catch:
> 
> In [2]: dts = [0, 0.5, 1.0, 1.5, 1.99, 2.0, 2.5, 3.0] * u.s
> In [3]: dates_utc = Time(Time('2015-06-30 23:59:59') + dts, scale='utc')
> In [4]: dates_tai = Time(dates_utc.iso, scale='tai')
> WARNING: ErfaWarning: ERFA function "dtf2d" yielded 3 of "time is after end of day (Note 5)" [astropy._erfa.core]
> In [5]: for date_utc, date_tai in zip(dates_utc, dates_tai):
>    ...:     print(f'{date_utc} {(date_utc - date_tai).sec:.2f}')
>    ...:     
> 2015-06-30 23:59:59.000 35.00
> 2015-06-30 23:59:59.500 35.00
> 2015-06-30 23:59:60.000 35.00
> 2015-06-30 23:59:60.500 35.00
> 2015-06-30 23:59:60.990 35.00
> 2015-07-01 00:00:00.000 36.00
> 2015-07-01 00:00:00.500 36.00
> 2015-07-01 00:00:01.000 36.00
>  
> 
> My code didn?t work at leap second either, but this code does:
> 
> def tai_from_utc(utc):
>     """Return TAI in unix seconds, given UTC in unix seconds.
>     """
>     astropy_utc = astropy.time.Time(utc, scale="utc", format="unix")
>     dt_utc = astropy_utc.utc.to_datetime()
>     dt_tai = astropy_utc.tai.to_datetime()
>     tai_minus_utc = (dt_tai - dt_utc).total_seconds()
>     return utc + tai_minus_utc
> 
> On this, I would caution against using the astropy unix format for calculations where the details matter.  From the TimeUnix API docs <https://docs.astropy.org/en/stable/api/astropy.time.TimeUnix.html#astropy.time.TimeUnix>:
> 
> NOTE: this quantity is not exactly unix time and differs from the strict POSIX definition by up to 1 second on days with a leap second. POSIX unix time actually jumps backward by 1 second at midnight on leap second days while this class value is monotonically increasing at 86400 seconds per UTC day.

I had missed that warning. Ouch!

I think I have been approaching this the wrong way. We are representing timestamps in TAI unix seconds. I have two cases:

1) Generate a TAI unix timestamp using the current time.

I really want to get this one right.

Originally I had hoped to use `Time.now().tai.unix`. Unfortunately that gives UTC, not TAI.

My fallback was `tai_from_utc(ttime.time()) but this is looking even worse, since it?s not completely clear what time.time() will return near the leap second (at least based on the wikipedia article on unix timestamps).

The wikipedia article on unix timestamps points out that the POSIX standard specifies one behavior for system time, but that systems that use NTP typically use a different standard (though one that includes useful flags). We?ll be using PTP or NTP. Unfortunately it may not be possible to use the time, datetime, and/or astropy.time packages as none of them appear to pay attention to those flags.

2) Convert a normal unix timestamp (as a float, any other information such as leap seconds flags is gone) to a TAI unix timestamp.

In this case we could probably live with a 1 second error at or near a leap second because the information is only used to measure delays in our messaging system (DDS). But if I can get it right, so much the better.

> I'm not sure about your test case, but the Python `datetime` does not support leap seconds.  I got this exception trying to run your code within a leap second, but maybe I did something differently:
> 
> ValueError: Time (array(2015, dtype=int32), array(6, dtype=int32), array(30, dtype=int32), array(23, dtype=int32), array(59, dtype=int32), array(60, dtype=int32), array(0, dtype=int32)) is within a leap second but datetime does not support leap seconds

That is very helpful. My test was missing ?fraction of a second before seconds=60?. With that I get the same error. Of course I can subtract a second from the two times when that error occurs, but it doesn?t help with the fundamental issues.

Regards,

Russell

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From peter.erwin at gmail.com  Sun Aug 25 16:11:11 2019
From: peter.erwin at gmail.com (Peter Erwin)
Date: Sun, 25 Aug 2019 22:11:11 +0200
Subject: [AstroPy] Preliminary/beta version of PyImfit
Message-ID: <B5596EC9-A169-4F79-BEB3-5251B8800EA8@gmail.com>

Hi,

I'd like to announce the availability of a preliminary version of PyImfit, a Python wrapper 
around the C++-based galaxy-image-fitting code Imfit 

Imfit is a fast, flexible system for fitting FITS image (of galaxies or other objects) with simple or 
complex sets of models, using optional PSF convolution (including convolution of sub-regions
using oversampled PSF images) with a choice of multiple fitting algorithms algorithms and several 
different fit statistics (e.g., standard chi^2 and pure Poisson-based). For more information, see:
	http://www.mpe.mpg.de/~erwin/code/imfit/

PyImfit allows the use of Imfit models and fitting from within Python, using Numpy arrays.

The full package (for Python 3.6 or later on macOS, 3.5 or later on Linux) can be found on 
Github at 
	https://github.com/perwin/pyimfit
and can also be installed via pip:
	$ pip3 install pyimfit
(On macOS, this will install a pre-compiled binary wheel. On Linux, it may be necessary
for your version of GCC to be 5.0 or newer.)

Limited documentation (currently being expanded) can be found here:
	https://pyimfit.readthedocs.io/en/latest/
This includes a Jupyter notebook which provides an example of using PyImfit with the MCMC 
package "emcee":
	https://github.com/perwin/pyimfit/blob/master/docs/pyimfit_emcee.ipynb

The documentation for Imfit will probably also be useful (e.g., currently the
only place where the image functions are described in detail):
	https://imfit.readthedocs.io/en/latest/
	http://www.mpe.mpg.de/~erwin/resources/imfit/imfit_howto.pdf


Questions, bug reports, and suggestions for improvement are very welcome;
you can email me (erwin at sigmaxi.net or erwin at mpe.mpg.de) or open an 
issue at the Github site (https://github.com/perwin/pyimfit/issues).

cheers,

Peter
=============================================================
Peter Erwin                   Max-Planck-Insitute for Extraterrestrial 
erwin at mpe.mpg.de              Physics, Giessenbachstrasse
tel. +49 (0)176 2481 7713     85748 Garching, Germany
fax  +49 (0)89 30000 3495     http://www.mpe.mpg.de/~erwin




From antigone.lambert-huyghe at cea.fr  Mon Aug 26 03:24:08 2019
From: antigone.lambert-huyghe at cea.fr (LAMBERT-HUYGHE Antigone)
Date: Mon, 26 Aug 2019 07:24:08 +0000
Subject: [AstroPy] Problem with the latest version of astropy and numpy
In-Reply-To: <CAAye0vs=maUhykP=4W1JpW1k+es4OcYkHW2CfL+QpzyxPk1BqA@mail.gmail.com>
References: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312AFCC@e-exdage-b0.extra.cea.fr>,
 <CAAye0vs=maUhykP=4W1JpW1k+es4OcYkHW2CfL+QpzyxPk1BqA@mail.gmail.com>
Message-ID: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C02D@e-exdage-b0.extra.cea.fr>

Hi,

I re-installed previous versions, more precisely 3.0.4 for astropy and 1.16.4 for numpy. The things are going well, with no error, and the convolution is well done, for any size of map. So I'm sure it is due to new versions of astropy (or numpy).

I don't understant why it should be a quantity, because I'm not using directly _result_as_quantity(), but astropy.convolution.convolve(), for which the doc is the following:

convolve(array, kernel, boundary='fill', fill_value=0.0, nan_treatment='interpolate', normalize_kernel=True, mask=None, preserve_nan=False, normalization_zero_tol=1e-08)

Parameters

array NDData<https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData> or numpy.ndarray<https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray> or array-like

The array to convolve. This should be a 1, 2, or 3-dimensional array or a list or a set of nested lists representing a 1, 2, or 3-dimensional array. If an NDData<https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData>, the mask of the NDData<https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData> will be used as the mask argument.

kernel numpy.ndarray<https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray> or Kernel<https://docs.astropy.org/en/stable/api/astropy.convolution.Kernel.html#astropy.convolution.Kernel>

The convolution kernel. The number of dimensions should match those for the array, and the dimensions should be odd in all directions. If a masked array, the masked values will be replaced by fill_value.

[...]
Returns

result numpy.ndarray<https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray>

An array with the same dimensions and as the input array, convolved with kernel. The data type depends on the input array type. If array is a floating point type, then the return array keeps the same data type, otherwise the type is numpy.float.

I don't understand why this function is now using _result_as_quantity(), from what I checked in the source code it is indirect use. But from the doc I can use numpy arrays as input for the map to convolve.

Best,

Antigone
________________________________
De : AstroPy [astropy-bounces+antigone.lambert-huyghe=cea.fr at python.org] de la part de Kenneth Anderson [kanderso at gemini.edu]
Envoy? : vendredi 23 ao?t 2019 17:04
? : Astronomical Python mailing list
Objet : Re: [AstroPy] Problem with the latest version of astropy and numpy

Hi Antigone,

I cannot be sure how this problem arises for you, but what can be said is that an AttributeError thrown from the numpy object is way off base for that function. According the docstr on the _result_as_quantity(), the return object, i.e. the  'out' object, should be an astropy.units.Quantity object, not a numpy object.

It is unclear where things got confused in the call stack: perhaps an incorrect object type was passed initially? You may want to absolutely ensure that this did work under the previous versions. And if so, then it would seem something is amiss in that astropy call stack.

>From the docstr:
---------------------
_result_as_quantity(self, result, unit, out):
        [ ... ]
        Parameters
        ----------
        result : `~numpy.ndarray` or tuple of `~numpy.ndarray`
            Array(s) which need to be turned into quantity.
        unit : `~astropy.units.Unit` or None
            Unit for the quantities to be returned (or `None` if the result
            should not be a quantity).  Should be tuple if result is a tuple.
        out : `~astropy.units.Quantity` or None
            Possible output quantity. Should be `None` or a tuple if result
            is a tuple.

        Returns
        -------
        out : `~astropy.units.Quantity`
           With units set.

salud,
k


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From simon at sconseil.fr  Mon Aug 26 05:59:04 2019
From: simon at sconseil.fr (Simon Conseil)
Date: Mon, 26 Aug 2019 11:59:04 +0200
Subject: [AstroPy] Problem with the latest version of astropy and numpy
In-Reply-To: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C02D@e-exdage-b0.extra.cea.fr>
References: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312AFCC@e-exdage-b0.extra.cea.fr>
 <CAAye0vs=maUhykP=4W1JpW1k+es4OcYkHW2CfL+QpzyxPk1BqA@mail.gmail.com>
 <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C02D@e-exdage-b0.extra.cea.fr>
Message-ID: <d345d7e3-6cda-d31a-e0f5-3e0d205338a2@sconseil.fr>

Hi,

It is indeed weird that it tries to convert to a quantity if you are 
using Numpy arrays. There were significant changes in the convolution 
sub-package in Astropy 3.2 so this is probably worth a bug report, and 
ideally adding a minimal example to reproduce the issue (showing how you 
build the kernel).

Best,

Simon

Le 26/08/2019 ? 09:24, LAMBERT-HUYGHE Antigone a ?crit?:
> Hi,
>
> I re-installed previous versions, more precisely 3.0.4 for astropy and 1.16.4 for numpy. The things are going well, with no error, and the convolution is well done, for any size of map. So I'm sure it is due to new versions of astropy (or numpy).
>
> I don't understant why it should be a quantity, because I'm not using directly _result_as_quantity(), but astropy.convolution.convolve(), for which the doc is the following:
>
> convolve(array, kernel, boundary='fill', fill_value=0.0, nan_treatment='interpolate', normalize_kernel=True, mask=None, preserve_nan=False, normalization_zero_tol=1e-08)
>
> Parameters
>
> array NDData<https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData> or numpy.ndarray<https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray> or array-like
>
> The array to convolve. This should be a 1, 2, or 3-dimensional array or a list or a set of nested lists representing a 1, 2, or 3-dimensional array. If an NDData<https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData>, the mask of the NDData<https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData> will be used as the mask argument.
>
> kernel numpy.ndarray<https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray> or Kernel<https://docs.astropy.org/en/stable/api/astropy.convolution.Kernel.html#astropy.convolution.Kernel>
>
> The convolution kernel. The number of dimensions should match those for the array, and the dimensions should be odd in all directions. If a masked array, the masked values will be replaced by fill_value.
>
> [...]
> Returns
>
> result numpy.ndarray<https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray>
>
> An array with the same dimensions and as the input array, convolved with kernel. The data type depends on the input array type. If array is a floating point type, then the return array keeps the same data type, otherwise the type is numpy.float.
>
> I don't understand why this function is now using _result_as_quantity(), from what I checked in the source code it is indirect use. But from the doc I can use numpy arrays as input for the map to convolve.
>
> Best,
>
> Antigone
> ________________________________
> De : AstroPy [astropy-bounces+antigone.lambert-huyghe=cea.fr at python.org] de la part de Kenneth Anderson [kanderso at gemini.edu]
> Envoy? : vendredi 23 ao?t 2019 17:04
> ? : Astronomical Python mailing list
> Objet : Re: [AstroPy] Problem with the latest version of astropy and numpy
>
> Hi Antigone,
>
> I cannot be sure how this problem arises for you, but what can be said is that an AttributeError thrown from the numpy object is way off base for that function. According the docstr on the _result_as_quantity(), the return object, i.e. the  'out' object, should be an astropy.units.Quantity object, not a numpy object.
>
> It is unclear where things got confused in the call stack: perhaps an incorrect object type was passed initially? You may want to absolutely ensure that this did work under the previous versions. And if so, then it would seem something is amiss in that astropy call stack.
>
>  From the docstr:
> ---------------------
> _result_as_quantity(self, result, unit, out):
>          [ ... ]
>          Parameters
>          ----------
>          result : `~numpy.ndarray` or tuple of `~numpy.ndarray`
>              Array(s) which need to be turned into quantity.
>          unit : `~astropy.units.Unit` or None
>              Unit for the quantities to be returned (or `None` if the result
>              should not be a quantity).  Should be tuple if result is a tuple.
>          out : `~astropy.units.Quantity` or None
>              Possible output quantity. Should be `None` or a tuple if result
>              is a tuple.
>
>          Returns
>          -------
>          out : `~astropy.units.Quantity`
>             With units set.
>
> salud,
> k
>
>
>
>
> _______________________________________________
> AstroPy mailing list
> AstroPy at python.org
> https://mail.python.org/mailman/listinfo/astropy
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From antigone.lambert-huyghe at cea.fr  Mon Aug 26 06:58:09 2019
From: antigone.lambert-huyghe at cea.fr (LAMBERT-HUYGHE Antigone)
Date: Mon, 26 Aug 2019 10:58:09 +0000
Subject: [AstroPy] Problem with the latest version of astropy and numpy
In-Reply-To: <d345d7e3-6cda-d31a-e0f5-3e0d205338a2@sconseil.fr>
References: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312AFCC@e-exdage-b0.extra.cea.fr>
 <CAAye0vs=maUhykP=4W1JpW1k+es4OcYkHW2CfL+QpzyxPk1BqA@mail.gmail.com>
 <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C02D@e-exdage-b0.extra.cea.fr>,
 <d345d7e3-6cda-d31a-e0f5-3e0d205338a2@sconseil.fr>
Message-ID: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C07F@e-exdage-b0.extra.cea.fr>

Hi,

Ok, where can I send the bug report? I will construct the minimal example ASAP.

Best,
Antigone
________________________________
De : AstroPy [astropy-bounces+antigone.lambert-huyghe=cea.fr at python.org] de la part de Simon Conseil [simon at sconseil.fr]
Envoy? : lundi 26 ao?t 2019 11:59
? : astropy at python.org
Objet : Re: [AstroPy] Problem with the latest version of astropy and numpy


Hi,

It is indeed weird that it tries to convert to a quantity if you are using Numpy arrays. There were significant changes in the convolution sub-package in Astropy 3.2 so this is probably worth a bug report, and ideally adding a minimal example to reproduce the issue (showing how you build the kernel).

Best,

Simon

Le 26/08/2019 ? 09:24, LAMBERT-HUYGHE Antigone a ?crit :

Hi,

I re-installed previous versions, more precisely 3.0.4 for astropy and 1.16.4 for numpy. The things are going well, with no error, and the convolution is well done, for any size of map. So I'm sure it is due to new versions of astropy (or numpy).

I don't understant why it should be a quantity, because I'm not using directly _result_as_quantity(), but astropy.convolution.convolve(), for which the doc is the following:

convolve(array, kernel, boundary='fill', fill_value=0.0, nan_treatment='interpolate', normalize_kernel=True, mask=None, preserve_nan=False, normalization_zero_tol=1e-08)

Parameters

array NDData<https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData><https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData> or numpy.ndarray<https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray><https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray> or array-like

The array to convolve. This should be a 1, 2, or 3-dimensional array or a list or a set of nested lists representing a 1, 2, or 3-dimensional array. If an NDData<https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData><https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData>, the mask of the NDData<https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData><https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData> will be used as the mask argument.

kernel numpy.ndarray<https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray><https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray> or Kernel<https://docs.astropy.org/en/stable/api/astropy.convolution.Kernel.html#astropy.convolution.Kernel><https://docs.astropy.org/en/stable/api/astropy.convolution.Kernel.html#astropy.convolution.Kernel>

The convolution kernel. The number of dimensions should match those for the array, and the dimensions should be odd in all directions. If a masked array, the masked values will be replaced by fill_value.

[...]
Returns

result numpy.ndarray<https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray><https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray>

An array with the same dimensions and as the input array, convolved with kernel. The data type depends on the input array type. If array is a floating point type, then the return array keeps the same data type, otherwise the type is numpy.float.

I don't understand why this function is now using _result_as_quantity(), from what I checked in the source code it is indirect use. But from the doc I can use numpy arrays as input for the map to convolve.

Best,

Antigone
________________________________
De : AstroPy [astropy-bounces+antigone.lambert-huyghe=cea.fr at python.org<mailto:astropy-bounces+antigone.lambert-huyghe=cea.fr at python.org>] de la part de Kenneth Anderson [kanderso at gemini.edu<mailto:kanderso at gemini.edu>]
Envoy? : vendredi 23 ao?t 2019 17:04
? : Astronomical Python mailing list
Objet : Re: [AstroPy] Problem with the latest version of astropy and numpy

Hi Antigone,

I cannot be sure how this problem arises for you, but what can be said is that an AttributeError thrown from the numpy object is way off base for that function. According the docstr on the _result_as_quantity(), the return object, i.e. the  'out' object, should be an astropy.units.Quantity object, not a numpy object.

It is unclear where things got confused in the call stack: perhaps an incorrect object type was passed initially? You may want to absolutely ensure that this did work under the previous versions. And if so, then it would seem something is amiss in that astropy call stack.

>From the docstr:
---------------------
_result_as_quantity(self, result, unit, out):
        [ ... ]
        Parameters
        ----------
        result : `~numpy.ndarray` or tuple of `~numpy.ndarray`
            Array(s) which need to be turned into quantity.
        unit : `~astropy.units.Unit` or None
            Unit for the quantities to be returned (or `None` if the result
            should not be a quantity).  Should be tuple if result is a tuple.
        out : `~astropy.units.Quantity` or None
            Possible output quantity. Should be `None` or a tuple if result
            is a tuple.

        Returns
        -------
        out : `~astropy.units.Quantity`
           With units set.

salud,
k







_______________________________________________
AstroPy mailing list
AstroPy at python.org<mailto:AstroPy at python.org>
https://mail.python.org/mailman/listinfo/astropy

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From simon at sconseil.fr  Mon Aug 26 08:22:31 2019
From: simon at sconseil.fr (Simon Conseil)
Date: Mon, 26 Aug 2019 14:22:31 +0200
Subject: [AstroPy] Problem with the latest version of astropy and numpy
In-Reply-To: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C07F@e-exdage-b0.extra.cea.fr>
References: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312AFCC@e-exdage-b0.extra.cea.fr>
 <CAAye0vs=maUhykP=4W1JpW1k+es4OcYkHW2CfL+QpzyxPk1BqA@mail.gmail.com>
 <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C02D@e-exdage-b0.extra.cea.fr>
 <d345d7e3-6cda-d31a-e0f5-3e0d205338a2@sconseil.fr>
 <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C07F@e-exdage-b0.extra.cea.fr>
Message-ID: <36aab5ae-e434-652b-d701-62493b7485bf@sconseil.fr>

The issue tracker is on github:

https://github.com/astropy/astropy/issues/new

Simon


Le 26/08/2019 ? 12:58, LAMBERT-HUYGHE Antigone a ?crit?:
> Hi,
>
> Ok, where can I send the bug report? I will construct the minimal example ASAP.
>
> Best,
> Antigone
> ________________________________
> De : AstroPy [astropy-bounces+antigone.lambert-huyghe=cea.fr at python.org] de la part de Simon Conseil [simon at sconseil.fr]
> Envoy? : lundi 26 ao?t 2019 11:59
> ? : astropy at python.org
> Objet : Re: [AstroPy] Problem with the latest version of astropy and numpy
>
>
> Hi,
>
> It is indeed weird that it tries to convert to a quantity if you are using Numpy arrays. There were significant changes in the convolution sub-package in Astropy 3.2 so this is probably worth a bug report, and ideally adding a minimal example to reproduce the issue (showing how you build the kernel).
>
> Best,
>
> Simon
>
> Le 26/08/2019 ? 09:24, LAMBERT-HUYGHE Antigone a ?crit :
>
> Hi,
>
> I re-installed previous versions, more precisely 3.0.4 for astropy and 1.16.4 for numpy. The things are going well, with no error, and the convolution is well done, for any size of map. So I'm sure it is due to new versions of astropy (or numpy).
>
> I don't understant why it should be a quantity, because I'm not using directly _result_as_quantity(), but astropy.convolution.convolve(), for which the doc is the following:
>
> convolve(array, kernel, boundary='fill', fill_value=0.0, nan_treatment='interpolate', normalize_kernel=True, mask=None, preserve_nan=False, normalization_zero_tol=1e-08)
>
> Parameters
>
> array NDData<https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData><https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData> or numpy.ndarray<https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray><https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray> or array-like
>
> The array to convolve. This should be a 1, 2, or 3-dimensional array or a list or a set of nested lists representing a 1, 2, or 3-dimensional array. If an NDData<https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData><https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData>, the mask of the NDData<https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData><https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData> will be used as the mask argument.
>
> kernel numpy.ndarray<https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray><https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray> or Kernel<https://docs.astropy.org/en/stable/api/astropy.convolution.Kernel.html#astropy.convolution.Kernel><https://docs.astropy.org/en/stable/api/astropy.convolution.Kernel.html#astropy.convolution.Kernel>
>
> The convolution kernel. The number of dimensions should match those for the array, and the dimensions should be odd in all directions. If a masked array, the masked values will be replaced by fill_value.
>
> [...]
> Returns
>
> result numpy.ndarray<https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray><https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray>
>
> An array with the same dimensions and as the input array, convolved with kernel. The data type depends on the input array type. If array is a floating point type, then the return array keeps the same data type, otherwise the type is numpy.float.
>
> I don't understand why this function is now using _result_as_quantity(), from what I checked in the source code it is indirect use. But from the doc I can use numpy arrays as input for the map to convolve.
>
> Best,
>
> Antigone
> ________________________________
> De : AstroPy [astropy-bounces+antigone.lambert-huyghe=cea.fr at python.org<mailto:astropy-bounces+antigone.lambert-huyghe=cea.fr at python.org>] de la part de Kenneth Anderson [kanderso at gemini.edu<mailto:kanderso at gemini.edu>]
> Envoy? : vendredi 23 ao?t 2019 17:04
> ? : Astronomical Python mailing list
> Objet : Re: [AstroPy] Problem with the latest version of astropy and numpy
>
> Hi Antigone,
>
> I cannot be sure how this problem arises for you, but what can be said is that an AttributeError thrown from the numpy object is way off base for that function. According the docstr on the _result_as_quantity(), the return object, i.e. the  'out' object, should be an astropy.units.Quantity object, not a numpy object.
>
> It is unclear where things got confused in the call stack: perhaps an incorrect object type was passed initially? You may want to absolutely ensure that this did work under the previous versions. And if so, then it would seem something is amiss in that astropy call stack.
>
>  From the docstr:
> ---------------------
> _result_as_quantity(self, result, unit, out):
>          [ ... ]
>          Parameters
>          ----------
>          result : `~numpy.ndarray` or tuple of `~numpy.ndarray`
>              Array(s) which need to be turned into quantity.
>          unit : `~astropy.units.Unit` or None
>              Unit for the quantities to be returned (or `None` if the result
>              should not be a quantity).  Should be tuple if result is a tuple.
>          out : `~astropy.units.Quantity` or None
>              Possible output quantity. Should be `None` or a tuple if result
>              is a tuple.
>
>          Returns
>          -------
>          out : `~astropy.units.Quantity`
>             With units set.
>
> salud,
> k
>
>
>
>
>
>
>
> _______________________________________________
> 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
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From antigone.lambert-huyghe at cea.fr  Mon Aug 26 08:24:51 2019
From: antigone.lambert-huyghe at cea.fr (LAMBERT-HUYGHE Antigone)
Date: Mon, 26 Aug 2019 12:24:51 +0000
Subject: [AstroPy] Problem with the latest version of astropy and numpy
In-Reply-To: <36aab5ae-e434-652b-d701-62493b7485bf@sconseil.fr>
References: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312AFCC@e-exdage-b0.extra.cea.fr>
 <CAAye0vs=maUhykP=4W1JpW1k+es4OcYkHW2CfL+QpzyxPk1BqA@mail.gmail.com>
 <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C02D@e-exdage-b0.extra.cea.fr>
 <d345d7e3-6cda-d31a-e0f5-3e0d205338a2@sconseil.fr>
 <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C07F@e-exdage-b0.extra.cea.fr>,
 <36aab5ae-e434-652b-d701-62493b7485bf@sconseil.fr>
Message-ID: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C09F@e-exdage-b0.extra.cea.fr>

Isn't there an other way? I don't have a github account.

Antigone
________________________________
De : AstroPy [astropy-bounces+antigone.lambert-huyghe=cea.fr at python.org] de la part de Simon Conseil [simon at sconseil.fr]
Envoy? : lundi 26 ao?t 2019 14:22
? : astropy at python.org
Objet : Re: [AstroPy] Problem with the latest version of astropy and numpy


The issue tracker is on github:

https://github.com/astropy/astropy/issues/new

Simon


Le 26/08/2019 ? 12:58, LAMBERT-HUYGHE Antigone a ?crit :

Hi,

Ok, where can I send the bug report? I will construct the minimal example ASAP.

Best,
Antigone
________________________________
De : AstroPy [astropy-bounces+antigone.lambert-huyghe=cea.fr at python.org<mailto:astropy-bounces+antigone.lambert-huyghe=cea.fr at python.org>] de la part de Simon Conseil [simon at sconseil.fr<mailto:simon at sconseil.fr>]
Envoy? : lundi 26 ao?t 2019 11:59
? : astropy at python.org<mailto:astropy at python.org>
Objet : Re: [AstroPy] Problem with the latest version of astropy and numpy


Hi,

It is indeed weird that it tries to convert to a quantity if you are using Numpy arrays. There were significant changes in the convolution sub-package in Astropy 3.2 so this is probably worth a bug report, and ideally adding a minimal example to reproduce the issue (showing how you build the kernel).

Best,

Simon

Le 26/08/2019 ? 09:24, LAMBERT-HUYGHE Antigone a ?crit :

Hi,

I re-installed previous versions, more precisely 3.0.4 for astropy and 1.16.4 for numpy. The things are going well, with no error, and the convolution is well done, for any size of map. So I'm sure it is due to new versions of astropy (or numpy).

I don't understant why it should be a quantity, because I'm not using directly _result_as_quantity(), but astropy.convolution.convolve(), for which the doc is the following:

convolve(array, kernel, boundary='fill', fill_value=0.0, nan_treatment='interpolate', normalize_kernel=True, mask=None, preserve_nan=False, normalization_zero_tol=1e-08)

Parameters

array NDData<https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData><https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData><https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData><https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData> or numpy.ndarray<https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray><https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray><https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray><https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray> or array-like

The array to convolve. This should be a 1, 2, or 3-dimensional array or a list or a set of nested lists representing a 1, 2, or 3-dimensional array. If an NDData<https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData><https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData><https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData><https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData>, the mask of the NDData<https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData><https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData><https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData><https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData> will be used as the mask argument.

kernel numpy.ndarray<https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray><https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray><https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray><https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray> or Kernel<https://docs.astropy.org/en/stable/api/astropy.convolution.Kernel.html#astropy.convolution.Kernel><https://docs.astropy.org/en/stable/api/astropy.convolution.Kernel.html#astropy.convolution.Kernel><https://docs.astropy.org/en/stable/api/astropy.convolution.Kernel.html#astropy.convolution.Kernel><https://docs.astropy.org/en/stable/api/astropy.convolution.Kernel.html#astropy.convolution.Kernel>

The convolution kernel. The number of dimensions should match those for the array, and the dimensions should be odd in all directions. If a masked array, the masked values will be replaced by fill_value.

[...]
Returns

result numpy.ndarray<https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray><https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray><https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray><https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray>

An array with the same dimensions and as the input array, convolved with kernel. The data type depends on the input array type. If array is a floating point type, then the return array keeps the same data type, otherwise the type is numpy.float.

I don't understand why this function is now using _result_as_quantity(), from what I checked in the source code it is indirect use. But from the doc I can use numpy arrays as input for the map to convolve.

Best,

Antigone
________________________________
De : AstroPy [astropy-bounces+antigone.lambert-huyghe=cea.fr at python.org<mailto:astropy-bounces+antigone.lambert-huyghe=cea.fr at python.org><mailto:astropy-bounces+antigone.lambert-huyghe=cea.fr at python.org><mailto:astropy-bounces+antigone.lambert-huyghe=cea.fr at python.org>] de la part de Kenneth Anderson [kanderso at gemini.edu<mailto:kanderso at gemini.edu><mailto:kanderso at gemini.edu><mailto:kanderso at gemini.edu>]
Envoy? : vendredi 23 ao?t 2019 17:04
? : Astronomical Python mailing list
Objet : Re: [AstroPy] Problem with the latest version of astropy and numpy

Hi Antigone,

I cannot be sure how this problem arises for you, but what can be said is that an AttributeError thrown from the numpy object is way off base for that function. According the docstr on the _result_as_quantity(), the return object, i.e. the  'out' object, should be an astropy.units.Quantity object, not a numpy object.

It is unclear where things got confused in the call stack: perhaps an incorrect object type was passed initially? You may want to absolutely ensure that this did work under the previous versions. And if so, then it would seem something is amiss in that astropy call stack.

>From the docstr:
---------------------
_result_as_quantity(self, result, unit, out):
        [ ... ]
        Parameters
        ----------
        result : `~numpy.ndarray` or tuple of `~numpy.ndarray`
            Array(s) which need to be turned into quantity.
        unit : `~astropy.units.Unit` or None
            Unit for the quantities to be returned (or `None` if the result
            should not be a quantity).  Should be tuple if result is a tuple.
        out : `~astropy.units.Quantity` or None
            Possible output quantity. Should be `None` or a tuple if result
            is a tuple.

        Returns
        -------
        out : `~astropy.units.Quantity`
           With units set.

salud,
k







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https://mail.python.org/mailman/listinfo/astropy






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From aldcroft at head.cfa.harvard.edu  Mon Aug 26 08:51:32 2019
From: aldcroft at head.cfa.harvard.edu (Aldcroft, Thomas)
Date: Mon, 26 Aug 2019 08:51:32 -0400
Subject: [AstroPy] Problem with the latest version of astropy and numpy
In-Reply-To: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C09F@e-exdage-b0.extra.cea.fr>
References: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312AFCC@e-exdage-b0.extra.cea.fr>
 <CAAye0vs=maUhykP=4W1JpW1k+es4OcYkHW2CfL+QpzyxPk1BqA@mail.gmail.com>
 <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C02D@e-exdage-b0.extra.cea.fr>
 <d345d7e3-6cda-d31a-e0f5-3e0d205338a2@sconseil.fr>
 <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C07F@e-exdage-b0.extra.cea.fr>
 <36aab5ae-e434-652b-d701-62493b7485bf@sconseil.fr>
 <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C09F@e-exdage-b0.extra.cea.fr>
Message-ID: <CAMtEP6xzM4WxN9gBY2Mt8uqFn_4oaegR9uCjBPBfuwtSjQcTZg@mail.gmail.com>

Feel free to post the example here and a maintainer will put it on GitHub
for you.

Thanks!
Tom

On Mon, Aug 26, 2019 at 8:25 AM LAMBERT-HUYGHE Antigone <
antigone.lambert-huyghe at cea.fr> wrote:

> Isn't there an other way? I don't have a github account.
>
> Antigone
> ------------------------------
> *De :* AstroPy [astropy-bounces+antigone.lambert-huyghe=cea.fr at python.org]
> de la part de Simon Conseil [simon at sconseil.fr]
> *Envoy? :* lundi 26 ao?t 2019 14:22
> *? :* astropy at python.org
> *Objet :* Re: [AstroPy] Problem with the latest version of astropy and
> numpy
>
> The issue tracker is on github:
>
> https://github.com/astropy/astropy/issues/new
>
> Simon
>
>
> Le 26/08/2019 ? 12:58, LAMBERT-HUYGHE Antigone a ?crit :
>
> Hi,
>
> Ok, where can I send the bug report? I will construct the minimal example ASAP.
>
> Best,
> Antigone
> ________________________________
> De : AstroPy [astropy-bounces+antigone.lambert-huyghe=cea.fr at python.org] de la part de Simon Conseil [simon at sconseil.fr]
> Envoy? : lundi 26 ao?t 2019 11:59
> ? : astropy at python.org
> Objet : Re: [AstroPy] Problem with the latest version of astropy and numpy
>
>
> Hi,
>
> It is indeed weird that it tries to convert to a quantity if you are using Numpy arrays. There were significant changes in the convolution sub-package in Astropy 3.2 so this is probably worth a bug report, and ideally adding a minimal example to reproduce the issue (showing how you build the kernel).
>
> Best,
>
> Simon
>
> Le 26/08/2019 ? 09:24, LAMBERT-HUYGHE Antigone a ?crit :
>
> Hi,
>
> I re-installed previous versions, more precisely 3.0.4 for astropy and 1.16.4 for numpy. The things are going well, with no error, and the convolution is well done, for any size of map. So I'm sure it is due to new versions of astropy (or numpy).
>
> I don't understant why it should be a quantity, because I'm not using directly _result_as_quantity(), but astropy.convolution.convolve(), for which the doc is the following:
>
> convolve(array, kernel, boundary='fill', fill_value=0.0, nan_treatment='interpolate', normalize_kernel=True, mask=None, preserve_nan=False, normalization_zero_tol=1e-08)
>
> Parameters
>
> array NDData<https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData> <https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData><https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData> <https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData> or numpy.ndarray<https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray> <https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray><https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray> <https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray> or array-like
>
> The array to convolve. This should be a 1, 2, or 3-dimensional array or a list or a set of nested lists representing a 1, 2, or 3-dimensional array. If an NDData<https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData> <https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData><https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData> <https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData>, the mask of the NDData<https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData> <https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData><https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData> <https://docs.astropy.org/en/stable/api/astropy.nddata.NDData.html#astropy.nddata.NDData> will be used as the mask argument.
>
> kernel numpy.ndarray<https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray> <https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray><https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray> <https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray> or Kernel<https://docs.astropy.org/en/stable/api/astropy.convolution.Kernel.html#astropy.convolution.Kernel> <https://docs.astropy.org/en/stable/api/astropy.convolution.Kernel.html#astropy.convolution.Kernel><https://docs.astropy.org/en/stable/api/astropy.convolution.Kernel.html#astropy.convolution.Kernel> <https://docs.astropy.org/en/stable/api/astropy.convolution.Kernel.html#astropy.convolution.Kernel>
>
> The convolution kernel. The number of dimensions should match those for the array, and the dimensions should be odd in all directions. If a masked array, the masked values will be replaced by fill_value.
>
> [...]
> Returns
>
> result numpy.ndarray<https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray> <https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray><https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray> <https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray>
>
> An array with the same dimensions and as the input array, convolved with kernel. The data type depends on the input array type. If array is a floating point type, then the return array keeps the same data type, otherwise the type is numpy.float.
>
> I don't understand why this function is now using _result_as_quantity(), from what I checked in the source code it is indirect use. But from the doc I can use numpy arrays as input for the map to convolve.
>
> Best,
>
> Antigone
> ________________________________
> De : AstroPy [astropy-bounces+antigone.lambert-huyghe=cea.fr at python.org<mailto:astropy-bounces+antigone.lambert-huyghe=cea.fr at python.org> <astropy-bounces+antigone.lambert-huyghe=cea.fr at python.org>] de la part de Kenneth Anderson [kanderso at gemini.edu<mailto:kanderso at gemini.edu> <kanderso at gemini.edu>]
> Envoy? : vendredi 23 ao?t 2019 17:04
> ? : Astronomical Python mailing list
> Objet : Re: [AstroPy] Problem with the latest version of astropy and numpy
>
> Hi Antigone,
>
> I cannot be sure how this problem arises for you, but what can be said is that an AttributeError thrown from the numpy object is way off base for that function. According the docstr on the _result_as_quantity(), the return object, i.e. the  'out' object, should be an astropy.units.Quantity object, not a numpy object.
>
> It is unclear where things got confused in the call stack: perhaps an incorrect object type was passed initially? You may want to absolutely ensure that this did work under the previous versions. And if so, then it would seem something is amiss in that astropy call stack.
>
> From the docstr:
> ---------------------
> _result_as_quantity(self, result, unit, out):
>         [ ... ]
>         Parameters
>         ----------
>         result : `~numpy.ndarray` or tuple of `~numpy.ndarray`
>             Array(s) which need to be turned into quantity.
>         unit : `~astropy.units.Unit` or None
>             Unit for the quantities to be returned (or `None` if the result
>             should not be a quantity).  Should be tuple if result is a tuple.
>         out : `~astropy.units.Quantity` or None
>             Possible output quantity. Should be `None` or a tuple if result
>             is a tuple.
>
>         Returns
>         -------
>         out : `~astropy.units.Quantity`
>            With units set.
>
> salud,
> k
>
>
>
>
>
>
>
> _______________________________________________
> AstroPy mailing listAstroPy at python.org<mailto:AstroPy at python.org> <AstroPy at python.org>https://mail.python.org/mailman/listinfo/astropy
>
>
> _______________________________________________
> AstroPy mailing listAstroPy at python.orghttps://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 antigone.lambert-huyghe at cea.fr  Mon Aug 26 09:16:47 2019
From: antigone.lambert-huyghe at cea.fr (LAMBERT-HUYGHE Antigone)
Date: Mon, 26 Aug 2019 13:16:47 +0000
Subject: [AstroPy] Problem with the latest version of astropy and numpy
In-Reply-To: <CAMtEP6xzM4WxN9gBY2Mt8uqFn_4oaegR9uCjBPBfuwtSjQcTZg@mail.gmail.com>
References: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312AFCC@e-exdage-b0.extra.cea.fr>
 <CAAye0vs=maUhykP=4W1JpW1k+es4OcYkHW2CfL+QpzyxPk1BqA@mail.gmail.com>
 <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C02D@e-exdage-b0.extra.cea.fr>
 <d345d7e3-6cda-d31a-e0f5-3e0d205338a2@sconseil.fr>
 <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C07F@e-exdage-b0.extra.cea.fr>
 <36aab5ae-e434-652b-d701-62493b7485bf@sconseil.fr>
 <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C09F@e-exdage-b0.extra.cea.fr>,
 <CAMtEP6xzM4WxN9gBY2Mt8uqFn_4oaegR9uCjBPBfuwtSjQcTZg@mail.gmail.com>
Message-ID: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C0C6@e-exdage-b0.extra.cea.fr>

So I report here the problem as a bug.

Here is the minimal example of my problem (with the imports) :

import astropy.units as u
from astropy.convolution import convolve
import numpy as np
from astropy.io import fits
from astropy.convolution import Gaussian2DKernel
from copy import deepcopy

#The aim is to convolve the map in the file file.fits from a resolution of 1.6 arcsec to 6 arcsec
inhdu = fits.open('file.fits')

fromfwhm = 1.6*u.arcsec
tofwhm = 6*u.arcsec

#calculate kernel size
f2s = 2.*np.sqrt(2*np.log(2))

pixel_size = (abs(inhdu[0].header['CDELT1']) *u.deg).to('arcsec')
#CDELT is a keyword in the header that gives the size of the pixel in an angular unit.

kernel_sigma = np.sqrt( (tofwhm)**2 - (fromfwhm)**2 ) / pixel_size / f2s

kernel = Gaussian2DKernel(stddev=kernel_sigma)

result = convolve(inhdu[0].data, kernel, boundary = 'fill', fill_value = float('NaN'), preserve_nan=True)

outhdu = hdudeepcopy(inhdu)
outhdu[0].data = result

outhdu.writeto(WriteTo, overwrite=True)

And, as a reminder, here is the error that I had:

~/Bureau/Codes/python_lib/mylib/fits.py in fits_convolve(infits, fromfwhm, tofwhm, GaussianTrim, WriteTo, pixkey, pixkey_unit, returnHDU, verbose)
    640             result[i, :, :] = convolve(plane, kernel, boundary = 'fill', fill_value = float('NaN'), preserve_nan=True)
    641     else:
--> 642         result = convolve(inhdu[0].data, kernel, boundary = 'fill', fill_value = float('NaN'), preserve_nan=True)
    643         #result = convolve_fft(inhdu[0].data, kernel)
    644

~/.local/lib/python3.6/site-packages/astropy/nddata/decorators.py in wrapper(data, *args, **kwargs)
    244                                   AstropyUserWarning)
    245
--> 246             result = func(data, *args, **kwargs)
    247
    248             if unpack and repack:

~/.local/lib/python3.6/site-packages/astropy/convolution/convolve.py in convolve(array, kernel, boundary, fill_value, nan_treatment, normalize_kernel, mask, preserve_nan, normalization_zero_tol)
    336     if normalize_kernel:
    337         if not nan_interpolate:
--> 338             result /= kernel_sum
    339     else:
    340         if nan_interpolate:

~/.local/lib/python3.6/site-packages/astropy/units/quantity.py in __array_ufunc__(self, function, method, *inputs, **kwargs)
    473             return result
    474
--> 475         return self._result_as_quantity(result, unit, out)
    476
    477     def _result_as_quantity(self, result, unit, out):

~/.local/lib/python3.6/site-packages/astropy/units/quantity.py in _result_as_quantity(self, result, unit, out)
    512         # the output is of the correct Quantity subclass, as it was passed
    513         # through check_output.
--> 514         out._set_unit(unit)
    515         return out
    516

AttributeError: 'numpy.ndarray' object has no attribute '_set_unit'

Thank you for all the answeres that I had here.
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From simon at sconseil.fr  Mon Aug 26 11:04:58 2019
From: simon at sconseil.fr (Simon Conseil)
Date: Mon, 26 Aug 2019 17:04:58 +0200
Subject: [AstroPy] Problem with the latest version of astropy and numpy
In-Reply-To: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C0C6@e-exdage-b0.extra.cea.fr>
References: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312AFCC@e-exdage-b0.extra.cea.fr>
 <CAAye0vs=maUhykP=4W1JpW1k+es4OcYkHW2CfL+QpzyxPk1BqA@mail.gmail.com>
 <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C02D@e-exdage-b0.extra.cea.fr>
 <d345d7e3-6cda-d31a-e0f5-3e0d205338a2@sconseil.fr>
 <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C07F@e-exdage-b0.extra.cea.fr>
 <36aab5ae-e434-652b-d701-62493b7485bf@sconseil.fr>
 <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C09F@e-exdage-b0.extra.cea.fr>
 <CAMtEP6xzM4WxN9gBY2Mt8uqFn_4oaegR9uCjBPBfuwtSjQcTZg@mail.gmail.com>
 <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C0C6@e-exdage-b0.extra.cea.fr>
Message-ID: <9e7c70e0-5986-52d3-a8d8-e9c9217ea476@sconseil.fr>

https://github.com/astropy/astropy/issues/9168

As mentioned in the ticket, you use units for the kernel (kernel.array 
is a Quantity) so at least this explains why the crash happen in a 
quantity method.

Simon

Le 26/08/2019 ? 15:16, LAMBERT-HUYGHE Antigone a ?crit?:
> So I report here the problem as a bug.
>
> Here is the minimal example of my problem (with the imports) :
>
> import astropy.units as u
> from astropy.convolution import convolve
> import numpy as np
> from astropy.io import fits
> from astropy.convolution import Gaussian2DKernel
> from copy import deepcopy
>
> #The aim is to convolve the map in the file file.fits from a resolution of 1.6 arcsec to 6 arcsec
> inhdu = fits.open('file.fits')
>
> fromfwhm = 1.6*u.arcsec
> tofwhm = 6*u.arcsec
>
> #calculate kernel size
> f2s = 2.*np.sqrt(2*np.log(2))
>
> pixel_size = (abs(inhdu[0].header['CDELT1']) *u.deg).to('arcsec')
> #CDELT is a keyword in the header that gives the size of the pixel in an angular unit.
>
> kernel_sigma = np.sqrt( (tofwhm)**2 - (fromfwhm)**2 ) / pixel_size / f2s
>
> kernel = Gaussian2DKernel(stddev=kernel_sigma)
>
> result = convolve(inhdu[0].data, kernel, boundary = 'fill', fill_value = float('NaN'), preserve_nan=True)
>
> outhdu = hdudeepcopy(inhdu)
> outhdu[0].data = result
>
> outhdu.writeto(WriteTo, overwrite=True)
>
> And, as a reminder, here is the error that I had:
>
> ~/Bureau/Codes/python_lib/mylib/fits.py in fits_convolve(infits, fromfwhm, tofwhm, GaussianTrim, WriteTo, pixkey, pixkey_unit, returnHDU, verbose)
>      640             result[i, :, :] = convolve(plane, kernel, boundary = 'fill', fill_value = float('NaN'), preserve_nan=True)
>      641     else:
> --> 642         result = convolve(inhdu[0].data, kernel, boundary = 'fill', fill_value = float('NaN'), preserve_nan=True)
>      643         #result = convolve_fft(inhdu[0].data, kernel)
>      644
>
> ~/.local/lib/python3.6/site-packages/astropy/nddata/decorators.py in wrapper(data, *args, **kwargs)
>      244                                   AstropyUserWarning)
>      245
> --> 246             result = func(data, *args, **kwargs)
>      247
>      248             if unpack and repack:
>
> ~/.local/lib/python3.6/site-packages/astropy/convolution/convolve.py in convolve(array, kernel, boundary, fill_value, nan_treatment, normalize_kernel, mask, preserve_nan, normalization_zero_tol)
>      336     if normalize_kernel:
>      337         if not nan_interpolate:
> --> 338             result /= kernel_sum
>      339     else:
>      340         if nan_interpolate:
>
> ~/.local/lib/python3.6/site-packages/astropy/units/quantity.py in __array_ufunc__(self, function, method, *inputs, **kwargs)
>      473             return result
>      474
> --> 475         return self._result_as_quantity(result, unit, out)
>      476
>      477     def _result_as_quantity(self, result, unit, out):
>
> ~/.local/lib/python3.6/site-packages/astropy/units/quantity.py in _result_as_quantity(self, result, unit, out)
>      512         # the output is of the correct Quantity subclass, as it was passed
>      513         # through check_output.
> --> 514         out._set_unit(unit)
>      515         return out
>      516
>
> AttributeError: 'numpy.ndarray' object has no attribute '_set_unit'
>
> Thank you for all the answeres that I had here.
>
>
> _______________________________________________
> AstroPy mailing list
> AstroPy at python.org
> https://mail.python.org/mailman/listinfo/astropy
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From antigone.lambert-huyghe at cea.fr  Tue Aug 27 03:24:40 2019
From: antigone.lambert-huyghe at cea.fr (LAMBERT-HUYGHE Antigone)
Date: Tue, 27 Aug 2019 07:24:40 +0000
Subject: [AstroPy] Problem with the latest version of astropy and numpy
In-Reply-To: <9e7c70e0-5986-52d3-a8d8-e9c9217ea476@sconseil.fr>
References: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312AFCC@e-exdage-b0.extra.cea.fr>
 <CAAye0vs=maUhykP=4W1JpW1k+es4OcYkHW2CfL+QpzyxPk1BqA@mail.gmail.com>
 <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C02D@e-exdage-b0.extra.cea.fr>
 <d345d7e3-6cda-d31a-e0f5-3e0d205338a2@sconseil.fr>
 <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C07F@e-exdage-b0.extra.cea.fr>
 <36aab5ae-e434-652b-d701-62493b7485bf@sconseil.fr>
 <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C09F@e-exdage-b0.extra.cea.fr>
 <CAMtEP6xzM4WxN9gBY2Mt8uqFn_4oaegR9uCjBPBfuwtSjQcTZg@mail.gmail.com>
 <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C0C6@e-exdage-b0.extra.cea.fr>,
 <9e7c70e0-5986-52d3-a8d8-e9c9217ea476@sconseil.fr>
Message-ID: <A04EC7BAE538C148A4B6A95FFDFCCCAF3312C100@e-exdage-b0.extra.cea.fr>

Ok, thank you very much. I didn't know that a kernel was a quantity.

Antigone
________________________________
De : AstroPy [astropy-bounces+antigone.lambert-huyghe=cea.fr at python.org] de la part de Simon Conseil [simon at sconseil.fr]
Envoy? : lundi 26 ao?t 2019 17:04
? : astropy at python.org
Objet : Re: [AstroPy] Problem with the latest version of astropy and numpy


https://github.com/astropy/astropy/issues/9168

As mentioned in the ticket, you use units for the kernel (kernel.array is a Quantity) so at least this explains why the crash happen in a quantity method.

Simon

Le 26/08/2019 ? 15:16, LAMBERT-HUYGHE Antigone a ?crit :

So I report here the problem as a bug.

Here is the minimal example of my problem (with the imports) :

import astropy.units as u
from astropy.convolution import convolve
import numpy as np
from astropy.io import fits
from astropy.convolution import Gaussian2DKernel
from copy import deepcopy

#The aim is to convolve the map in the file file.fits from a resolution of 1.6 arcsec to 6 arcsec
inhdu = fits.open('file.fits')

fromfwhm = 1.6*u.arcsec
tofwhm = 6*u.arcsec

#calculate kernel size
f2s = 2.*np.sqrt(2*np.log(2))

pixel_size = (abs(inhdu[0].header['CDELT1']) *u.deg).to('arcsec')
#CDELT is a keyword in the header that gives the size of the pixel in an angular unit.

kernel_sigma = np.sqrt( (tofwhm)**2 - (fromfwhm)**2 ) / pixel_size / f2s

kernel = Gaussian2DKernel(stddev=kernel_sigma)

result = convolve(inhdu[0].data, kernel, boundary = 'fill', fill_value = float('NaN'), preserve_nan=True)

outhdu = hdudeepcopy(inhdu)
outhdu[0].data = result

outhdu.writeto(WriteTo, overwrite=True)

And, as a reminder, here is the error that I had:

~/Bureau/Codes/python_lib/mylib/fits.py in fits_convolve(infits, fromfwhm, tofwhm, GaussianTrim, WriteTo, pixkey, pixkey_unit, returnHDU, verbose)
    640             result[i, :, :] = convolve(plane, kernel, boundary = 'fill', fill_value = float('NaN'), preserve_nan=True)
    641     else:
--> 642         result = convolve(inhdu[0].data, kernel, boundary = 'fill', fill_value = float('NaN'), preserve_nan=True)
    643         #result = convolve_fft(inhdu[0].data, kernel)
    644

~/.local/lib/python3.6/site-packages/astropy/nddata/decorators.py in wrapper(data, *args, **kwargs)
    244                                   AstropyUserWarning)
    245
--> 246             result = func(data, *args, **kwargs)
    247
    248             if unpack and repack:

~/.local/lib/python3.6/site-packages/astropy/convolution/convolve.py in convolve(array, kernel, boundary, fill_value, nan_treatment, normalize_kernel, mask, preserve_nan, normalization_zero_tol)
    336     if normalize_kernel:
    337         if not nan_interpolate:
--> 338             result /= kernel_sum
    339     else:
    340         if nan_interpolate:

~/.local/lib/python3.6/site-packages/astropy/units/quantity.py in __array_ufunc__(self, function, method, *inputs, **kwargs)
    473             return result
    474
--> 475         return self._result_as_quantity(result, unit, out)
    476
    477     def _result_as_quantity(self, result, unit, out):

~/.local/lib/python3.6/site-packages/astropy/units/quantity.py in _result_as_quantity(self, result, unit, out)
    512         # the output is of the correct Quantity subclass, as it was passed
    513         # through check_output.
--> 514         out._set_unit(unit)
    515         return out
    516

AttributeError: 'numpy.ndarray' object has no attribute '_set_unit'

Thank you for all the answeres that I had here.





_______________________________________________
AstroPy mailing list
AstroPy at python.org<mailto:AstroPy at python.org>
https://mail.python.org/mailman/listinfo/astropy

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From gordon.b.dennis at gmail.com  Tue Aug 27 08:13:04 2019
From: gordon.b.dennis at gmail.com (Gordon Dennis)
Date: Tue, 27 Aug 2019 13:13:04 +0100
Subject: [AstroPy] Histogram problem in astropy tutorial
Message-ID: <000001d55cd0$c7efeb80$57cfc280$@gmail.com>

Hi everybody

I'm having some difficulty with the example 'Galaxy mass' in the tutorial at
http://learn.astropy.org/rst-tutorials/quantities.html?highlight=filtertutor
ials 

These lines are to setup matplotlib:

import matplotlib.pyplot as plt

%matplotlib inline

Spyder will not accept the second (i.e. %matplotlib inline) because,
according to a Stack Overflow answer 'Line magics are only supported by the
IPython command line. They cannot be used inside a script, because
%something is not correct Python syntax'.

Suggestion is to use

exec(%matplotlib inline)

This is accepted by the Python interpreter but doesn't work, i.e. the
subsequent code

plt.figure()

plt.hist(v, bins='auto', histtype="step")

plt.ylabel("N")

. does not produce the histogram expected.  The variable v is calculated
earlier in the code.

 

All the rest of the code works exactly as expected.  I've added input
statements to vary Reff and vmean in order to observe the effect of varying
these parameters and the results from the code check out against results
using a calculator.

I'm using Spyder 3 on Windows 10, fully patched.

Does anyone know of a way around this histogram problem?

Best regards

Gordon Dennis

 

 

+44(0)1934 838096 / +44(0)7774628110 / Skype: gordon.dennis

Sent from my Analytical Engine

Description: analyticalEngine

 

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From hulingyi1995 at yahoo.com.sg  Tue Aug 27 09:55:36 2019
From: hulingyi1995 at yahoo.com.sg (Lingyi Hu)
Date: Tue, 27 Aug 2019 21:55:36 +0800
Subject: [AstroPy] Histogram problem in astropy tutorial
In-Reply-To: <000001d55cd0$c7efeb80$57cfc280$@gmail.com>
References: <000001d55cd0$c7efeb80$57cfc280$@gmail.com>
Message-ID: <CAApfPRxK4Mke2HaYmsLHWPtVL4prtWK2ekWNbS_J1NOGfQbCww@mail.gmail.com>

Hi Gordon,

I believe you can do a normal plt.show() at the end of plotting to show the
graph. Don't think you need the exec(%matplotlib inline) if you are not in
ipython. I don't use Spyder but apparently there are some settings you can
set in Spyder to make it work like a IPython notebook:
https://stackoverflow.com/questions/23585126/how-do-i-get-interactive-plots-again-in-spyder-ipython-matplotlib

Lingyi

On Tue, Aug 27, 2019 at 8:13 PM Gordon Dennis <gordon.b.dennis at gmail.com>
wrote:

> Hi everybody
>
> I'm having some difficulty with the example 'Galaxy mass' in the tutorial
> at
> http://learn.astropy.org/rst-tutorials/quantities.html?highlight=filtertutorials
>
> These lines are to setup matplotlib:
>
> import matplotlib.pyplot as plt
>
> %matplotlib inline
>
> Spyder will not accept the second (i.e. %matplotlib inline) because,
> according to a Stack Overflow answer 'Line magics are only supported by the
> IPython command line. They cannot be used inside a script, because
> %something is not correct Python syntax'.
>
> Suggestion is to use
>
> exec(%matplotlib inline)
>
> This is accepted by the Python interpreter but doesn't work, i.e. the
> subsequent code
>
> plt.figure()
>
> plt.hist(v, bins='auto', histtype="step")
>
> plt.ylabel("N")
>
> ? does not produce the histogram expected.  The variable v is calculated
> earlier in the code.
>
>
>
> All the rest of the code works exactly as expected.  I've added input
> statements to vary Reff and vmean in order to observe the effect of varying
> these parameters and the results from the code check out against results
> using a calculator.
>
> I?m using Spyder 3 on Windows 10, fully patched.
>
> Does anyone know of a way around this histogram problem?
>
> Best regards
>
> Gordon Dennis
>
>
>
>
>
> +44(0)1934 838096 / +44(0)7774628110 / Skype: gordon.dennis
>
> Sent from my Analytical Engine
>
> [image: Description: analyticalEngine]
>
>
> _______________________________________________
> AstroPy mailing list
> AstroPy at python.org
> https://mail.python.org/mailman/listinfo/astropy
>
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From dstansby at gmail.com  Tue Aug 27 10:10:28 2019
From: dstansby at gmail.com (David Stansby)
Date: Tue, 27 Aug 2019 15:10:28 +0100
Subject: [AstroPy] Histogram problem in astropy tutorial
In-Reply-To: <000001d55cd0$c7efeb80$57cfc280$@gmail.com>
References: <000001d55cd0$c7efeb80$57cfc280$@gmail.com>
Message-ID: <CAGm9cHCnAc0hvrBLr-3OAxri7wvRzUo5ZfhzwVwL3wukf3tjeg@mail.gmail.com>

Hi Gordon,

If you're using Matplotlib in a normal python session then you don't need
the '%matplotlib inline' command, but you will need to append 'plt.show()`
to the end of your script to make the figure show up.

Cheers,
David

On Tue, 27 Aug 2019 at 13:13, Gordon Dennis <gordon.b.dennis at gmail.com>
wrote:

> Hi everybody
>
> I'm having some difficulty with the example 'Galaxy mass' in the tutorial
> at
> http://learn.astropy.org/rst-tutorials/quantities.html?highlight=filtertutorials
>
> These lines are to setup matplotlib:
>
> import matplotlib.pyplot as plt
>
> %matplotlib inline
>
> Spyder will not accept the second (i.e. %matplotlib inline) because,
> according to a Stack Overflow answer 'Line magics are only supported by the
> IPython command line. They cannot be used inside a script, because
> %something is not correct Python syntax'.
>
> Suggestion is to use
>
> exec(%matplotlib inline)
>
> This is accepted by the Python interpreter but doesn't work, i.e. the
> subsequent code
>
> plt.figure()
>
> plt.hist(v, bins='auto', histtype="step")
>
> plt.ylabel("N")
>
> ? does not produce the histogram expected.  The variable v is calculated
> earlier in the code.
>
>
>
> All the rest of the code works exactly as expected.  I've added input
> statements to vary Reff and vmean in order to observe the effect of varying
> these parameters and the results from the code check out against results
> using a calculator.
>
> I?m using Spyder 3 on Windows 10, fully patched.
>
> Does anyone know of a way around this histogram problem?
>
> Best regards
>
> Gordon Dennis
>
>
>
>
>
> +44(0)1934 838096 / +44(0)7774628110 / Skype: gordon.dennis
>
> Sent from my Analytical Engine
>
> [image: Description: analyticalEngine]
>
>
> _______________________________________________
> AstroPy mailing list
> AstroPy at python.org
> https://mail.python.org/mailman/listinfo/astropy
>
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From gordon.b.dennis at gmail.com  Tue Aug 27 15:22:25 2019
From: gordon.b.dennis at gmail.com (Gordon Dennis)
Date: Tue, 27 Aug 2019 20:22:25 +0100
Subject: [AstroPy] AstroPy Digest, Vol 155, Issue 14
In-Reply-To: <mailman.967.1566915043.30343.astropy@python.org>
References: <mailman.967.1566915043.30343.astropy@python.org>
Message-ID: <001e01d55d0c$c2c74e50$4855eaf0$@gmail.com>

Hi everyone

A couple of people suggested the usual plt.show()after the third line, but
that doesn't change anything I'm afraid - the histogram still doesn't work
as the example shows.

Anybody any other suggestions please?.

Best regards

Gordon

 

-----Original Message-----
From: AstroPy [mailto:astropy-bounces+gordon.b.dennis=gmail.com at python.org]
On Behalf Of astropy-request at python.org
Sent: Tuesday, August 27, 2019 15:11
To: astropy at python.org
Subject: AstroPy Digest, Vol 155, Issue 14

 

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Today's Topics:

 

   1. Re: Histogram problem in astropy tutorial (Lingyi Hu)

   2. Re: Histogram problem in astropy tutorial (David Stansby)

 

 

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

 

Message: 1

Date: Tue, 27 Aug 2019 21:55:36 +0800

From: Lingyi Hu <hulingyi1995 at yahoo.com.sg>

To: Astronomical Python mailing list <astropy at python.org>

Subject: Re: [AstroPy] Histogram problem in astropy tutorial

Message-ID:

 
<CAApfPRxK4Mke2HaYmsLHWPtVL4prtWK2ekWNbS_J1NOGfQbCww at mail.gmail.com>

Content-Type: text/plain; charset="utf-8"

 

Hi Gordon,

 

I believe you can do a normal plt.show() at the end of plotting to show the
graph. Don't think you need the exec(%matplotlib inline) if you are not in
ipython. I don't use Spyder but apparently there are some settings you can
set in Spyder to make it work like a IPython notebook:

 
<https://stackoverflow.com/questions/23585126/how-do-i-get-interactive-plots
-again-in-spyder-ipython-matplotlib>
https://stackoverflow.com/questions/23585126/how-do-i-get-interactive-plots-
again-in-spyder-ipython-matplotlib

 

Lingyi

 

On Tue, Aug 27, 2019 at 8:13 PM Gordon Dennis <
<mailto:gordon.b.dennis at gmail.com> gordon.b.dennis at gmail.com>

wrote:

 

> Hi everybody

> 

> I'm having some difficulty with the example 'Galaxy mass' in the 

> tutorial at 

>  <http://learn.astropy.org/rst-tutorials/quantities.html?highlight=filte>
http://learn.astropy.org/rst-tutorials/quantities.html?highlight=filte

> rtutorials

> 

> These lines are to setup matplotlib:

> 

> import matplotlib.pyplot as plt

> 

> %matplotlib inline

> 

> Spyder will not accept the second (i.e. %matplotlib inline) because, 

> according to a Stack Overflow answer 'Line magics are only supported 

> by the IPython command line. They cannot be used inside a script, 

> because %something is not correct Python syntax'.

> 

> Suggestion is to use

> 

> exec(%matplotlib inline)

> 

> This is accepted by the Python interpreter but doesn't work, i.e. the 

> subsequent code

> 

> plt.figure()

> 

> plt.hist(v, bins='auto', histtype="step")

> 

> plt.ylabel("N")

> 

> ? does not produce the histogram expected.  The variable v is 

> calculated earlier in the code.

> 

> 

> 

> All the rest of the code works exactly as expected.  I've added input 

> statements to vary Reff and vmean in order to observe the effect of 

> varying these parameters and the results from the code check out 

> against results using a calculator.

> 

> I?m using Spyder 3 on Windows 10, fully patched.

> 

> Does anyone know of a way around this histogram problem?

> 

> Best regards

> 

> Gordon Dennis

> 

> 

> 

> 

> 

> +44(0)1934 838096 / +44(0)7774628110 / Skype: gordon.dennis

> 

> Sent from my Analytical Engine

> 

> [image: Description: analyticalEngine]

> 

> 

> _______________________________________________

> AstroPy mailing list

>  <mailto:AstroPy at python.org> AstroPy at python.org

>  <https://mail.python.org/mailman/listinfo/astropy>
https://mail.python.org/mailman/listinfo/astropy

> 

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Message: 2

Date: Tue, 27 Aug 2019 15:10:28 +0100

From: David Stansby <dstansby at gmail.com>

To: Astronomical Python mailing list <astropy at python.org>

Subject: Re: [AstroPy] Histogram problem in astropy tutorial

Message-ID:

 
<CAGm9cHCnAc0hvrBLr-3OAxri7wvRzUo5ZfhzwVwL3wukf3tjeg at mail.gmail.com>

Content-Type: text/plain; charset="utf-8"

 

Hi Gordon,

 

If you're using Matplotlib in a normal python session then you don't need
the '%matplotlib inline' command, but you will need to append 'plt.show()`
to the end of your script to make the figure show up.

 

Cheers,

David

 

On Tue, 27 Aug 2019 at 13:13, Gordon Dennis <
<mailto:gordon.b.dennis at gmail.com> gordon.b.dennis at gmail.com>

wrote:

 

> Hi everybody

> 

> I'm having some difficulty with the example 'Galaxy mass' in the 

> tutorial at 

>  <http://learn.astropy.org/rst-tutorials/quantities.html?highlight=filte>
http://learn.astropy.org/rst-tutorials/quantities.html?highlight=filte

> rtutorials

> 

> These lines are to setup matplotlib:

> 

> import matplotlib.pyplot as plt

> 

> %matplotlib inline

> 

> Spyder will not accept the second (i.e. %matplotlib inline) because, 

> according to a Stack Overflow answer 'Line magics are only supported 

> by the IPython command line. They cannot be used inside a script, 

> because %something is not correct Python syntax'.

> 

> Suggestion is to use

> 

> exec(%matplotlib inline)

> 

> This is accepted by the Python interpreter but doesn't work, i.e. the 

> subsequent code

> 

> plt.figure()

> 

> plt.hist(v, bins='auto', histtype="step")

> 

> plt.ylabel("N")

> 

> ? does not produce the histogram expected.  The variable v is 

> calculated earlier in the code.

> 

> 

> 

> All the rest of the code works exactly as expected.  I've added input 

> statements to vary Reff and vmean in order to observe the effect of 

> varying these parameters and the results from the code check out 

> against results using a calculator.

> 

> I?m using Spyder 3 on Windows 10, fully patched.

> 

> Does anyone know of a way around this histogram problem?

> 

> Best regards

> 

> Gordon Dennis

> 

> 

> 

> 

> 

> +44(0)1934 838096 / +44(0)7774628110 / Skype: gordon.dennis

> 

> Sent from my Analytical Engine

> 

> [image: Description: analyticalEngine]

> 

> 

> _______________________________________________

> AstroPy mailing list

>  <mailto:AstroPy at python.org> AstroPy at python.org

>  <https://mail.python.org/mailman/listinfo/astropy>
https://mail.python.org/mailman/listinfo/astropy

> 

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From wtylergee at gmail.com  Tue Aug 27 16:17:37 2019
From: wtylergee at gmail.com (Wilfred Tyler Gee)
Date: Wed, 28 Aug 2019 06:17:37 +1000
Subject: [AstroPy] Histogram problem in astropy tutorial
In-Reply-To: <CAGm9cHCnAc0hvrBLr-3OAxri7wvRzUo5ZfhzwVwL3wukf3tjeg@mail.gmail.com>
References: <000001d55cd0$c7efeb80$57cfc280$@gmail.com>
 <CAGm9cHCnAc0hvrBLr-3OAxri7wvRzUo5ZfhzwVwL3wukf3tjeg@mail.gmail.com>
Message-ID: <CAESfxSDJ8bV6FVdtczZfQyXk9=U2HN3geMpfV6S-vOdr=OCcsA@mail.gmail.com>

Hi Gordon,

Just to be clear, this is not a problem with the histogram but with the
environment and how it is being called. Spyder is a different environment
from a jupyter notebook and the tutorial is specifically using a notebook.

That said, Spyder does (I believe) have a mechanism for plotting within the
IDE itself. Most likely you just remove the line about the  matplotlib
magic.

Cheers,

On Wed, Aug 28, 2019, 00:11 David Stansby <dstansby at gmail.com> wrote:

> Hi Gordon,
>
> If you're using Matplotlib in a normal python session then you don't need
> the '%matplotlib inline' command, but you will need to append 'plt.show()`
> to the end of your script to make the figure show up.
>
> Cheers,
> David
>
> On Tue, 27 Aug 2019 at 13:13, Gordon Dennis <gordon.b.dennis at gmail.com>
> wrote:
>
>> Hi everybody
>>
>> I'm having some difficulty with the example 'Galaxy mass' in the tutorial
>> at
>> http://learn.astropy.org/rst-tutorials/quantities.html?highlight=filtertutorials
>>
>> These lines are to setup matplotlib:
>>
>> import matplotlib.pyplot as plt
>>
>> %matplotlib inline
>>
>> Spyder will not accept the second (i.e. %matplotlib inline) because,
>> according to a Stack Overflow answer 'Line magics are only supported by the
>> IPython command line. They cannot be used inside a script, because
>> %something is not correct Python syntax'.
>>
>> Suggestion is to use
>>
>> exec(%matplotlib inline)
>>
>> This is accepted by the Python interpreter but doesn't work, i.e. the
>> subsequent code
>>
>> plt.figure()
>>
>> plt.hist(v, bins='auto', histtype="step")
>>
>> plt.ylabel("N")
>>
>> ? does not produce the histogram expected.  The variable v is calculated
>> earlier in the code.
>>
>>
>>
>> All the rest of the code works exactly as expected.  I've added input
>> statements to vary Reff and vmean in order to observe the effect of varying
>> these parameters and the results from the code check out against results
>> using a calculator.
>>
>> I?m using Spyder 3 on Windows 10, fully patched.
>>
>> Does anyone know of a way around this histogram problem?
>>
>> Best regards
>>
>> Gordon Dennis
>>
>>
>>
>>
>>
>> +44(0)1934 838096 / +44(0)7774628110 / Skype: gordon.dennis
>>
>> Sent from my Analytical Engine
>>
>> [image: Description: analyticalEngine]
>>
>>
>> _______________________________________________
>> 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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