chiantipy-users — Discussion list for ChiantiPy users

[Chiantipy-users] Variable thermal module

[LIAISIAN A. <abd...@gm...>]

Dear all,

I'm new user of Chiantipy and i have a question:
Is there some function, which can be called directly from chianti library
that allows to extract the input and output (parameters/functions) of
Variable Thermal module? It's called vth in IDL version.

Thank you in advance.

Sincerely,
Liaisian

Re: [Chiantipy-users] Free Bound intensity zero when using Spectrum

[Ken D. <kd...@gm...>]

Hi Urvashi Gupta,


thanks for your interest in CHIANTI and ChiantiPy.


First, in order to understand your problem, please tell us exactly what 
commands your are using.


Second, the latest versions of ChiantiPy are only available on github:


https://github.com/chianti-atomic/ChiantiPy


and the documentation on


http://chiantipy.readthedocs.io/en/latest/


but I don't think that should change the result you are getting.


best regards

Ken


On 06/14/2017 12:51 PM, URVASHI GUPTA wrote:
>
> Hello,
>
>
> I am new to ChiantiPy (Please bear with me) and have been trying to 
> learn how things work using the quick start guide. While trying to 
> replicate the results in one of the examples, I am running into a problem:
>
>
> I want to plot the Free Bound intensity using doContinuum=1 in the 
> spectrum class. While my Free Free intensity plot and spectrum turns 
> out perfectly fine, the Free Bound intensity plot is a flat line at 
> zero. I am not able to work this out as it certainly is not an issue 
> with the coding. I tried to verify the database structure but  nothing 
> looks fishy.
>
>
> I will be grateful if someone can guide me through this.
>
>
> Thanks & Regards
>
> Urvashi Gupta
>
>
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
> _______________________________________________
> Chiantipy-users mailing list
> Chi...@li...
> https://lists.sourceforge.net/lists/listinfo/chiantipy-users

-- 
Kenneth P. Dere
Research Professor of Solar Physics
Department of Physics and Astronomy
George Mason University
kd...@gm...

[Chiantipy-users] Free Bound intensity zero when using Spectrum

[URVASHI G. <ugu...@wi...>]

Hello,


I am new to ChiantiPy (Please bear with me) and have been trying to learn how things work using the quick start guide. While trying to replicate the results in one of the examples, I am running into a problem:


I want to plot the Free Bound intensity using doContinuum=1 in the spectrum class. While my Free Free intensity plot and spectrum turns out perfectly fine, the Free Bound intensity plot is a flat line at zero. I am not able to work this out as it certainly is not an issue with the coding. I tried to verify the database structure but  nothing looks fishy.


I will be grateful if someone can guide me through this.


Thanks & Regards

Urvashi Gupta

Re: [Chiantipy-users] OpenAstronomy in Google Summer of Code 2017

[Aniket P. <ann...@gm...>]

>
> Hello Tom,
>

        I've written my proposal for Astropy, can you please tell me on how 
I can get it reviewed by the mentors?

 Thanks 
 Aniket

[Chiantipy-users] OpenAstronomy in Google Summer of Code 2017

[Tom A. <tal...@gm...>]

On behalf of the OpenAstronomy organization I'm pleased to announce that we
have again been accepted as a mentoring organization in the Google Summer
of Code program.  Thus far we have potential project ideas from Astropy,
SunPy, and Glue.

*Students*

If you or someone you know is interested in participating in GSoC with
OpenAstronomy, please visit the following links to get started:

 GSoC OpenAstronomy page
<https://summerofcode.withgoogle.com/organizations/6364832820363264/>
 OpenAstronomy student guidelines
<http://openastronomy.org/gsoc/student_guidelines.html>
 OpenAstronomy project ideas <http://openastronomy.org/gsoc/gsoc2017/>

*More project ideas*

It is late, but not impossibly late, to add ideas for GSoC projects for
this year.  If you'd like to do so please add an issue to
https://github.com/OpenAstronomy/openastronomy.github.io and the admins
there will take it from there.  Note that one should definitely have at
least two committed mentors in mind for any project.

Cheers,
Tom A, on behalf of OpenAstronomy

Re: [Chiantipy-users] Disparity between normal and multiprocessing Synthetic Spectrum

[Ken D. <kd...@gm...>]

Hi Chris,

first, in your case, mspectrum should be invoked with em=dem. Maybe that 
is what you actually did.

The crash seems to involve the tinker package which is not imported at 
all by ChiantiPy.  Are you by chance using the

builtin IDE 'IDLE', because it is built on tkinter.  I never use that 
because I have not found it useful.

My suggestion would be to try running in a simple Python interactive session

 > python(2.7 or 3.X) -i

or a interactive IPython session

 > ipython(2 or 3) this is what I would suggest but the simple Python 
session does not require any further downloads.

I have also forwarded this to the CHIANTI google group where we are 
trying to use for future discussions.  The Sourceforge site will be 
closed down at some point.

All code developement is going at at github:

https://github.com/chianti-atomic/ChiantiPy//

the latest code can be downloaded from there.  The latest version 
(0.6.5) on Sourceforge should work for mpsectrum.

Hope this helps,

best regards,

Ken



On 01/31/2017 02:39 PM, Chris Osborne wrote:
> Hi all,
>
>
> I'm trying to generate synthetic spectra for a simulated plasma. I 
> have a list of temperatures, densities and DEM per temperature bin 
> calculated from my simulation parameters. I'm using these as an input 
> to the spectrum and mspectrum models. In the attached graph, the top 
> plot is the output from mspectrum and the bottom is from spectrum. I 
> would love the speed benefits of mspectrum (58s vs 420s), but the 
> output is different and it crashes with the following error after 
> processing 3 spectra:
>
> Exception ignored in: <bound method Image.__del__ of 
> <tkinter.PhotoImage object at 0x7f11f2895b70>>
> Traceback (most recent call last):
>   File "/usr/lib/python3.5/tkinter/__init__.py", line 3359, in __del__
>     self.tk.call('image', 'delete', self.name)
> RuntimeError: main thread is not in main loop
> Exception ignored in: <bound method Image.__del__ of 
> <tkinter.PhotoImage object at 0x7f11f32a0eb8>>
> Traceback (most recent call last):
>   File "/usr/lib/python3.5/tkinter/__init__.py", line 3359, in __del__
>     self.tk.call('image', 'delete', self.name)
> RuntimeError: main thread is not in main loop
> Tcl_AsyncDelete: async handler deleted by the wrong thread
> Exception ignored in: <bound method Image.__del__ of 
> <tkinter.PhotoImage object at 0x7f11f2895b70>>
> Traceback (most recent call last):
>   File "/usr/lib/python3.5/tkinter/__init__.py", line 3359, in __del__
>     self.tk.call('image', 'delete', self.name)
> RuntimeError: main thread is not in main loop
> Exception ignored in: <bound method Image.__del__ of 
> <tkinter.PhotoImage object at 0x7f11f2895b70>>
> Traceback (most recent call last):
>   File "/usr/lib/python3.5/tkinter/__init__.py", line 3359, in __del__
>     self.tk.call('image', 'delete', self.name)
> RuntimeError: main thread is not in main loop
> Exception ignored in: <bound method Image.__del__ of 
> <tkinter.PhotoImage object at 0x7f11f32a0eb8>>
> Traceback (most recent call last):
>   File "/usr/lib/python3.5/tkinter/__init__.py", line 3359, in __del__
>     self.tk.call('image', 'delete', self.name)
> RuntimeError: main thread is not in main loop
> Tcl_AsyncDelete: async handler deleted by the wrong thread
> Exception ignored in: <bound method Image.__del__ of 
> <tkinter.PhotoImage object at 0x7f11f32a0eb8>>
> Traceback (most recent call last):
>   File "/usr/lib/python3.5/tkinter/__init__.py", line 3359, in __del__
>     self.tk.call('image', 'delete', self.name)
> RuntimeError: main thread is not in main loop
> Tcl_AsyncDelete: async handler deleted by the wrong thread
>
> Am I doing anything obviously wrong? I've added a minimal example to 
> generate the attached plot to the bottom of this email. Additionally, 
> ipymspectrum just gives me a spectrum with 0 intensity.
>
> Many thanks,
>
> Chris
>
>
> Code:
>
>
> import numpy as np
> import matplotlib.pyplot as plt
> import chianti.core as ch
>
> temperature = np.array([10000, 12589.3, 15848.9, 19952.6, 25118.9, 
> 31622.8, 39810.7, 50118.7,
>                         63095.7, 79432.8, 100000, 125893, 158489, 
> 199526, 251189, 316228, 398107,
>                         501187, 630957])
> density = np.array([2.65817e+11, 5.851e+10, 4.70312e+10, 3.61635e+10, 
> 2.95748e+10, 2.38194e+10,
>                     1.84037e+10, 1.45854e+10, 1.16196e+10, 
> 9.19655e+09, 7.40595e+09, 5.81195e+09,
>                     4.53517e+09, 3.58534e+09, 2.82369e+09, 
> 2.22591e+09, 1.74408e+09, 1.34533e+09,
>                     1.06134e+09])
> dem = np.array([1.07986e+31, 1.82215e+23, 1.97504e+23, 1.15849e+23, 
> 7.50969e+22, 6.9985e+22,
>                 7.95815e+22, 5.16034e+22, 5.7736e+22, 4.56957e+22, 
> 2.8911e+22, 1.04684e+22,
>                 1.21946e+22, 2.02881e+22, 3.13491e+22, 5.21445e+22, 
> 9.34264e+22, 1.95467e+23,
>                 3.75808e+24])
>
> wvl = 160.0 + 0.1 * np.arange(1200)
>
> s1 = ch.mspectrum(temperature, density, wvl, em=em, doContinuum=0, 
> ionList=['mg_6', 'mg_7', 'fe_10',
> 'fe_11', 'fe_12',
> 'fe_14'], proc=4)
> s2= ch.spectrum(temperature, density, wvl, em=em, doContinuum=0, 
> ionList=['mg_6', 'mg_7', 'fe_10',
> 'fe_11', 'fe_12',
> 'fe_14'])
> plt.subplot(211)
> plt.plot(wvl, s1.Spectrum['integrated'])
> plt.subplot(212)
> plt.plot(wvl, s2.Spectrum['integrated'])
> plt.show()
>
>
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>
>
> _______________________________________________
> Chiantipy-users mailing list
> Chi...@li...
> https://lists.sourceforge.net/lists/listinfo/chiantipy-users

-- 
Kenneth P. Dere
Research Professor of Solar Physics
Department of Physics and Astronomy
George Mason University
kd...@gm...

[Chiantipy-users] Disparity between normal and multiprocessing Synthetic Spectrum

[Chris O. <208...@st...>]

Hi all,


I'm trying to generate synthetic spectra for a simulated plasma. I have 
a list of temperatures, densities and DEM per temperature bin calculated 
from my simulation parameters. I'm using these as an input to the 
spectrum and mspectrum models. In the attached graph, the top plot is 
the output from mspectrum and the bottom is from spectrum. I would love 
the speed benefits of mspectrum (58s vs 420s), but the output is 
different and it crashes with the following error after processing 3 
spectra:

Exception ignored in: <bound method Image.__del__ of <tkinter.PhotoImage 
object at 0x7f11f2895b70>>
Traceback (most recent call last):
   File "/usr/lib/python3.5/tkinter/__init__.py", line 3359, in __del__
     self.tk.call('image', 'delete', self.name)
RuntimeError: main thread is not in main loop
Exception ignored in: <bound method Image.__del__ of <tkinter.PhotoImage 
object at 0x7f11f32a0eb8>>
Traceback (most recent call last):
   File "/usr/lib/python3.5/tkinter/__init__.py", line 3359, in __del__
     self.tk.call('image', 'delete', self.name)
RuntimeError: main thread is not in main loop
Tcl_AsyncDelete: async handler deleted by the wrong thread
Exception ignored in: <bound method Image.__del__ of <tkinter.PhotoImage 
object at 0x7f11f2895b70>>
Traceback (most recent call last):
   File "/usr/lib/python3.5/tkinter/__init__.py", line 3359, in __del__
     self.tk.call('image', 'delete', self.name)
RuntimeError: main thread is not in main loop
Exception ignored in: <bound method Image.__del__ of <tkinter.PhotoImage 
object at 0x7f11f2895b70>>
Traceback (most recent call last):
   File "/usr/lib/python3.5/tkinter/__init__.py", line 3359, in __del__
     self.tk.call('image', 'delete', self.name)
RuntimeError: main thread is not in main loop
Exception ignored in: <bound method Image.__del__ of <tkinter.PhotoImage 
object at 0x7f11f32a0eb8>>
Traceback (most recent call last):
   File "/usr/lib/python3.5/tkinter/__init__.py", line 3359, in __del__
     self.tk.call('image', 'delete', self.name)
RuntimeError: main thread is not in main loop
Tcl_AsyncDelete: async handler deleted by the wrong thread
Exception ignored in: <bound method Image.__del__ of <tkinter.PhotoImage 
object at 0x7f11f32a0eb8>>
Traceback (most recent call last):
   File "/usr/lib/python3.5/tkinter/__init__.py", line 3359, in __del__
     self.tk.call('image', 'delete', self.name)
RuntimeError: main thread is not in main loop
Tcl_AsyncDelete: async handler deleted by the wrong thread

Am I doing anything obviously wrong? I've added a minimal example to 
generate the attached plot to the bottom of this email. Additionally, 
ipymspectrum just gives me a spectrum with 0 intensity.

Many thanks,

Chris


Code:


import numpy as np
import matplotlib.pyplot as plt
import chianti.core as ch

temperature = np.array([10000, 12589.3, 15848.9, 19952.6, 25118.9, 
31622.8, 39810.7, 50118.7,
                         63095.7, 79432.8, 100000, 125893, 158489, 
199526, 251189, 316228, 398107,
                         501187, 630957])
density = np.array([2.65817e+11, 5.851e+10, 4.70312e+10, 3.61635e+10, 
2.95748e+10, 2.38194e+10,
                     1.84037e+10, 1.45854e+10, 1.16196e+10, 9.19655e+09, 
7.40595e+09, 5.81195e+09,
                     4.53517e+09, 3.58534e+09, 2.82369e+09, 2.22591e+09, 
1.74408e+09, 1.34533e+09,
                     1.06134e+09])
dem = np.array([1.07986e+31, 1.82215e+23, 1.97504e+23, 1.15849e+23, 
7.50969e+22, 6.9985e+22,
                 7.95815e+22, 5.16034e+22, 5.7736e+22, 4.56957e+22, 
2.8911e+22, 1.04684e+22,
                 1.21946e+22, 2.02881e+22, 3.13491e+22, 5.21445e+22, 
9.34264e+22, 1.95467e+23,
                 3.75808e+24])

wvl = 160.0 + 0.1 * np.arange(1200)

s1 = ch.mspectrum(temperature, density, wvl, em=em, doContinuum=0, 
ionList=['mg_6', 'mg_7', 'fe_10',
'fe_11', 'fe_12',
'fe_14'], proc=4)
s2= ch.spectrum(temperature, density, wvl, em=em, doContinuum=0, 
ionList=['mg_6', 'mg_7', 'fe_10',
'fe_11', 'fe_12',
'fe_14'])
plt.subplot(211)
plt.plot(wvl, s1.Spectrum['integrated'])
plt.subplot(212)
plt.plot(wvl, s2.Spectrum['integrated'])
plt.show()

[Chiantipy-users] chiantipy version 0.6.5 has been released

[Ken D. <kd...@gm...>]

This release fixed a bug with continuum calculations. Ions for which the 
continuum can not be calculated are now ignored.

The new files are available on sourceforge:

https://sourceforge.net/projects/chiantipy/

and on the Python Package Index PyPI

https://pypi.python.org/pypi/ChiantiPy/0.6.5

I would also point out that most of the development of ChiantiPy is now 
begin done on github

https://github.com/chianti-atomic/ChiantiPy

best regards,

Ken

-- 
Kenneth P. Dere
Research Professor of Solar Physics
Department of Physics and Astronomy
George Mason University
kd...@gm...

[Chiantipy-users] Applications for Python in Astronomy 2017 Now Open

[Stuart M. <st...@ca...>]

Hello all,


Applications are now being accepted for the 2017 Python in Astronomy
conference. The conference will be held on 8th - 12th May 2017 at the
Lorentz Center in Leiden, the Netherlands.


Applications to attend Python in Astronomy 2017 are now open until
December 9th 2016: Application Form
<https://goo.gl/forms/D8Zydnqhssn1J7vn1>.


The Python in Astronomy conferences  aim to bring a wide variety of
people who currently use, develop or teach people about Python packages
in the context of all forms of Astronomy. Participant selection will be
made with the goal of growingthe Python in Astronomy community and we
particularly encourage requests to attend from junior astronomers and
people who are new to contributing to open source software. This
conference is neither intended to be an introduction to Python bootcamp
nor only for expert-level Python developers, but we do expect all
participants to have at least a basic familiarity with Python.


Stuart Mumford, SOC Chair

Matt Craig

Kelle Cruz

Daniela Huppenkothen

Abigail Stevens

Erik Tollerud

[Chiantipy-users] Python in Astronomy 2017 Conference

[Stuart M. <st...@ca...>]

Hello all,


The 2017 Python in Astronomy conference will be held on 8th - 12th May
2017 at the Lorentz Center in Leiden, the Netherlands. For more
information see http://openastronomy.org/pyastro/2017/.


Python in Astronomy 2017 aims to bring a wide variety of people who
currently use, develop or teach people about Python packages in the
context of all forms of Astronomy. The conference will include
presentations, tutorials, unconference sessions, and sprints. As well as
building the community around astronomical uses of Python, the
conference aims to improve collaboration and interoperability between
Python packages and share knowledge on Python packages and techniques.
It will also provide training and educational materials for users and
developers of Python packages.Participant selection will be made with
the goal of growingthe Python in Astronomy community and we particularly
encourage requests to attend from junior astronomers and people who are
new to contributing to open source software.


If you are interested in attending and/or have any questions about the
conference, please use this form: https://goo.gl/forms/4Y7CB3mDwB6SqgtH2.


Further, please nominate people who you think should might benefit from
attending and contributing to Python in Astronomy 2017 using this form:

https://goo.gl/forms/4Y7CB3mDwB6SqgtH2


<https://goo.gl/forms/4Y7CB3mDwB6SqgtH2>

Applications from interested participants will open Sept 12th.


Stuart Mumford,

on behalf of the 2017 SOC

[Chiantipy-users] And Google Summer of Code has ended this year!!!

[DVD PS <dps...@gm...>]

This year has been an amazing one! This year was the first one in which
we've participated as an independent organisation covering many of the
astronomy open source efforts under the Open Astronomy umbrella
organisation.

http://openastronomy.org/members/

Under the Open Astronomy organisation we have been accepted by Google
directly, while in previous years the different organisations had
participated under the Python Software Foundation or NumFocus.  This is
great because it gives us a higher visibility for students and in the open
source communities, and in addition other important advantages: we get some
compensation from Google and two of us will represent the organisation in
the Google Summer of Code mentor summit happening at the end of October.

We got 8 slots from Google, of which 5 went to Astropy and 3 to SunPy.
Sadly the other sub-organisations (yt, chiantipy, juliaAstro, ...) didn't
get any qualified student applicants this time but surely it will change in
the future. From these 8 slots, 7 of them passed the mid-term and all the 7
passed the final evaluation. The students, their projects and the mentors
are the following:

For the Astropy project:

Micky Costa: Astropy: Bridge Sherpa and astropy fitting
<http://myopensauceadventure.blogspot.co.uk/2016/08/dessert.html> (Tom
Aldcroft, Omar Laurino, and Moritz Guenther)

Olga Vorokh: Image processing and source detection in Gammapy
<https://github.com/search?p=1&q=author%3AOlgaVorokh+created%3A%222016-02-10+..+2016-08-23%22&ref=searchresults&type=Issues&utf8=%E2%9C%93>
(Johannes King and Christoph Deil)

Zé Vinícius: Implement PSF photometry for fitting several overlapping
objects at once <http://mirca.github.io/gsoc-astropy-final/> (Moritz
Guenter, Brigitta Sipocz, and Erik Tollerud)

Karl Vyhmeister: Scheduling capabilities for Astroplan
<http://kvyhastroplan.blogspot.com/2016/08/cleaning-up-and-documenting.html?>
(Brett Morris and Erik Tollerud)

For SunPy:

Tessa Wilkinson: Implementing AIA response function in Sunpy
<http://tdwilkinson.blogspot.co.uk/2016/08/aia-response-summary-this-is-my-final.html>
(Drew Leonard and Will Barnes)

Punyaslok Pattnaik: Improvements to the SunPy Database
<https://punyaslokpattnaik.wordpress.com/2016/08/22/its-already-time/>
(Stuart Mumford and Simon Liedtke)

Sudarshan Konge: Real Time Data Access and Visualisation tools
<https://sudonymousblog.wordpress.com/2016/08/19/gsoc-summary-post/> (David
Perez-Suarez and Jack Ireland)

You can still see all their trip that brought them till the end reading
their blogs, available at:

http://openastronomy.org/Universe_OA/

If you would like to give us suggestions on how to improve the program (to
us as an umbrella, or to Google itself) or you want to get more involved
either as a mentor or as a sub-organisation, do not hesitate to contact
us.  There's a lot that we can do better in the coming years!!

Thanks for all the summer!
David Perez-Suarez, Tom Aldcroft,  Erik Tollerud, Stuart Mumford

[Chiantipy-users] Fwd: Re: gofnt and the Selector Dialogue

[Ken D. <kd...@gm...>]

Hi Kyle

Ithink this will provide your answer.  It was in the 
chi...@li... list on sourceforge from July 2015.

I had a hard time finding it myself but I knew it was out there.

I should probably put it in the quickstart guide as all the 
documentation is currently being revised for a new release on GitHub.

If this doesn't help, please let me know.

best regards,

Ken


-------- Forwarded Message --------
Subject: 	Re: [Chiantipy-users] gofnt and the Selector Dialogue
Date: 	Wed, 29 Jul 2015 12:28:30 -0400
From: 	Ken Dere <kd...@gm...>
To: 	chi...@li..., 110...@st...



Hi Kyle,

There is a fairly straightforward way to do this but the documentation
is incomplete and does not cover this.

so you have your 'fe14' object.

  > fe14.intensity()

this will calculate a dictionary fe14.Intensity with the following keys:

  > fe14.Intensity.keys()

['em',
   'intensity',
   'wvl',
   'lvl2',
   'lvl1',
   'pretty2',
   'ionS',
   'avalue',
   'pretty1',
   'integrated',
   'obs']

and

  > fe14.Intensity['wvl'][:5] give you the first 5 wavelengths in the
dictionary

array([ 5304.4868,   444.2202,   484.8212,   429.5743,   467.4282])

what you want next is the index for the line at 264.789

  > idx = argmin(abs(fe14.Intensity['wvl'] - 264.789))

argmin is a numpy function

  > print('%i'%(idx.size))

prints out 1, so there is only one line selected.

  > print('%10.4f'%(fe14.Intensity['wvl'][idx]))

prints out 264.7889

the G(T) function is just

mygofnt = fe14.Intensity['intensity'][:,idx]/fe14.EDensity

fe14.EDensity is just the electron density that fe14 was created with

  > print('%12.2e'%(fe14.EDensity))

and you get

1.00e+09

If the spectral line you are interested is a blend, then things are a
bit more difficult.  I will try to write up something on that later.

best regards,

Ken





On 07/29/2015 07:17 AM, Kyle Martin wrote:
> Hi all,
>
> I'm an undergraduate student getting to grips with Python for a summer
> project and I've constructed a piece of code that requires looping
> through a line that goes like:
>
> fe14.gofnt(wvlRange = [264.78,264.80],top=1)
>
> The issue with this is that it requires me to interact with the selector
> dialogue every time I loop through this line of code which won't be
> practical if I have to loop through it many times. My supervisor knows
> there is a way around this in IDL but I'm not familiar enough with
> Chiantipy or Python in general to know of a shortcut. I've narrowed the
> wavelength range down until there is only one line in the interval and
> provided top = 1 but it still insists on interacting with the selector
> dialogue. If anyone can think of a way around this I would really
> appreciate it!
>
> Thanks,
>
> Kyle
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Chiantipy-users mailing list
> Chi...@li...
> https://lists.sourceforge.net/lists/listinfo/chiantipy-users

-- 
Kenneth P. Dere
Research Professor of Solar Physics
School of Physics, Astronomy and Computational Science
George Mason University
kd...@gm...


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https://lists.sourceforge.net/lists/listinfo/chiantipy-users

[Chiantipy-users] ChiantiPy in now on github

[Ken D. <kd...@gm...>]

ChiantiPy is now on github:

https://github.com/chianti-atomic/ChiantiPy

the version number is 0.6.5 but the latest released version is 0.6.4 and 
is still available on Sourceforge.

There have been a number of requests to put ChiantiPy on github so that 
some users/groups can use it, perhaps incorporate it into their own 
project, and, hopefully, improve it.

best regards,

Ken

-- 
Kenneth P. Dere
Research Professor of Solar Physics
Department of Physics and Astronomy
George Mason University
kd...@gm...

[Chiantipy-users] Open Astronomy has been accepted for GSOC 2016

[DVD PS <dps...@gm...>]

Hello everyone!!!

Great tnews!! and I cannot type for teh excitment I have in me!!!
This year open astronomy is being the umbrella for all these projects (and
maybe more that want to form part) for the Google Summer of Code.

https://summerofcode.withgoogle.com/organizations/?sp-search=open%20astronomy

Thanks to all the admins for the different organisations that helped with
the proposal, the website, mailing lists and of course, the mentors for
providing ideas.

Yuuuuuhuuuuuuuuuuuuuuuuuuuuuuu!!!!

David

[Chiantipy-users] ChiantiPy is now on GitHub

[Ken D. <kd...@gm...>]

A version of ChiantiPy labelled version 0.7.0 is now on github

https://github.com/chianti-atomic/ChiantiPy

some of you may have forked it in the past but there have been several times
when I had to do a basic restart from scratch.  Hopefully this one will last

best regards

Ken

-- 
Kenneth P. Dere
Research Professor of Solar Physics
Department of Computational and Data Sciences
George Mason University
kd...@gm...

[Chiantipy-users] Application from OpenAstronomy to Google Summer of Code submitted

[DVD PS <dps...@gm...>]

Hello everyone,

We've just submitted the application for Google Summer of Code as a
umbrella organisation that includes: SunPy, Astropy, yt-project, julia
astro and chiantipy.

We have to wait 10 days for Google resolution.

Thanks to everyone that has helped on the application process. You can find
the submitted version on the following repository:

https://github.com/OpenAstronomy/GSoC

Have a wonderful weekend!!
David

[Chiantipy-users] ChiantiPy on github - latest news

[Ken D. <kd...@gm...>]

Some of you may have already realized that ChiantiPy is on github. 
However, its configuration is not really acceptable.  I have been trying 
to take it back to its just born state but my inexperience with git and 
github have not allowed me to get the desired result.

So, I will be deleting the ChiantiPy site and recreating it shortly 
thereafter.  The recreated site will not immediately contain much of 
anything at the beginning.  I don't know how this affects those who have 
forked but I suspect they will have to kill their fork and redo.

Ken

-- 
Kenneth P. Dere
Research Professor of Solar Physics
Department of Computational and Data Sciences
George Mason University
kd...@gm...

[Chiantipy-users] New web pages for ChiantiPy v0.6.4

[Ken D. <kd...@gm...>]

I have uploaded revised web pages to reflect the current status with the 
latest ChiantiPy release (0.6.4)

http://chiantipy.sourceforge.net/

Ken Dere

-- 
Kenneth P. Dere
Research Professor of Solar Physics
Department of Computational and Data Sciences
George Mason University
kd...@gm...

[Chiantipy-users] ChiantiPy version 0.6.4 has been released

[Ken D. <kd...@gm...>]

This is mostly a bug fixed release.

Errors in calculating the proton excitation rates were fixed. Thanks to 
Giulio Del Zanna for pointing this out.

Other edits were to make the package compatible with both Python 2.7 and 3

The software can be found on the Sourceforge project page and on PyPl

best regards,

Ken

-- 
Kenneth P. Dere
Research Professor of Solar Physics
Department of Computational and Data Sciences
George Mason University
kd...@gm...

Re: [Chiantipy-users] v0.6.3 added to GitHub

[Ken D. <kd...@gm...>]

Hi Will,

I have started migrating to github but have encountered some problems.  
Will probably have to do a complete restart but github is definitely in 
the plans.

Ken

On 01/20/2016 12:10 AM, Will Barnes wrote:
> Hi Ken,
>
> Is there any chance that this bug fix (and subsequent fixes) will be committed to ChiantiPy on GitHub? Additionally, are there plans to move all of the development of ChiantiPy over to GitHub? It seems to be a pretty popular platform for several open source Python astronomy packages (e.g. SunPy, Astropy to name a few).
>
> Thanks,
>
> Will Barnes
> ------------------------------------------------------------------------------
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-- 
Kenneth P. Dere
Research Professor of Solar Physics
Department of Computational and Data Sciences
George Mason University
kd...@gm...

[Chiantipy-users] v0.6.3 added to GitHub

[Will B. <wt...@ri...>]

Hi Ken, 

Is there any chance that this bug fix (and subsequent fixes) will be committed to ChiantiPy on GitHub? Additionally, are there plans to move all of the development of ChiantiPy over to GitHub? It seems to be a pretty popular platform for several open source Python astronomy packages (e.g. SunPy, Astropy to name a few).

Thanks,

Will Barnes

[Chiantipy-users] ChiantiPy version 0.6.2 and 0.6.3 have been released

[Ken D. <kd...@gm...>]

This is a bugfix release for the Continuum.freeFree method.

v0.6.2 is meant to be used with IPython 2 and 3

v0.6.3 is meant to be used with IPython4/Jupyter

the can be obtained at https://sourceforge.net/projects/chiantipy/

Kenneth P. Dere
Research Professor of Solar Physics
Department of Computational and Data Sciences
George Mason University
kd...@gm...

Re: [Chiantipy-users] ChiantiPy version 0.6.2 and 0.6.3 have been released

[Ken D. <kd...@gm...>]

Tell you the truth, I forgot to check but looking at the code, mspectrum 
just import the continuum module so it should work

let me know if it doesn't

Ken

On 01/19/2016 01:28 PM, arpan.das wrote:
> Does the bug for chianti mspectrum is also fixed which i am using with 
> python 2.7 and the multiprocessing module!
>
> On Tuesday, January 19, 2016 at 6:41:16 PM UTC+1, Ken Dere wrote:
>
>     This is a bugfix release for the Continuum.freeFree method.
>
>     v0.6.2 is meant to be used with IPython 2 and 3
>
>     v0.6.3 is meant to be used with IPython4/Jupyter
>
>     the can be obtained at https://sourceforge.net/projects/chiantipy/
>     <https://sourceforge.net/projects/chiantipy/>
>
>     Kenneth P. Dere
>     Research Professor of Solar Physics
>     Department of Computational and Data Sciences
>     George Mason University
>     kd...@gmu.edu <javascript:>
>

-- 
Kenneth P. Dere
Research Professor of Solar Physics
Department of Computational and Data Sciences
George Mason University
kd...@gm...

[Chiantipy-users] possible problems with Numpy

[Ken D. <kd...@gm...>]

I recently upgraded my linux distribution and this installed Numpy 
version 1.8.0.  The problem was evident when importing chiantipy was 
that an error message was given saying that, in the end, "_flbas" could 
not be imported.  I upgraded my Numpy distribution to version 1.10.1 and 
this problem went away.

Ken

-- 
Kenneth P. Dere
Research Professor of Solar Physics
Department of Computational and Data Sciences
George Mason University
kd...@gm...

Re: [Chiantipy-users] [chiantipy:discussion] problem running commands from QuickStart webpage

[Ken D. <kd...@gm...>]

Hi Raghvendra,

ChiantiPy is not a translation of the CHIANTI IDL routines.

If you got the the API documentation, the epydoc version at:

http://chiantipy.sourceforge.net/epydoc/index.html

you can follow the various links to find the complete list of methods 
and functions.  For example, click on chianti.core.Ion and then go to 
ion and you will get a list of the methods of the *ion *class.

follow the chianti.io and it will lead you to all of the *io *functions 
for reading and writing various files.  For example, 
chianti.io.elvlcRead('ne_8') returns a dictionary of the energy level 
information.  so,

 > elvlc = chianti.io.elvlcRead('ne_8')

where elvlc['lvl'] gives the level numbering.

for akey in elvlc.keys():  print(akey)

should tell you the dictionary keys

you can always do a

dir(elvlc), or any other object (in Python, everything is an object).

However, you are not going to understand ChiantiPy without a basic 
knowledge of Python.

best regards,

Ken

On 11/18/2015 02:09 PM, raghvendra sahai wrote:
> Dear Ken,
>  i will try to get the Python manuals you suggest. but i think that 
> won't tell me if there are additional commands in ChiantiPy that are 
> not listed on your Quick Start page. BTW, have ALL the commands in the 
> Chianti IDL version been translated into ChiantiPy (or does ChiantiPy 
> only have a subset of the most important ones)?
>
> thanks
> raghvendra
>
> On 11/17/2015 10:34 AM, Ken Dere wrote:
>> Hi Raghvendra,
>>
>> there is no real conversion from CHIANTI IDL to ChiantiPy. ChiantiPy 
>> is mostly object
>> oriented.
>>
>> Get a copy of Learning Python by Mark Lutz.  It has gotten to be a 
>> big book but it is
>> necessary to read a bit.  Also  the 'Python Pocket Reference' , by 
>> the same author, s
>> alway good to have at your side.
>>
>> best regards,
>>
>> Ken
>>
>> On 11/17/2015 12:34 PM, Sahai, Raghvendra (3263) wrote:
>>> Hi Ken
>>>   I guess you've solved the problem of getting the email to my address
>>>  I'm aware of the CHIANTI USER GUIDE, however, as I said in my 
>>> email, I don't know what
>>> the syntax of the commands in Chianti Py will be. Is there an easy 
>>> translation between
>>> the IDL and the python commands? I guess I can try looking at the 
>>> python source files
>>> (unfortunately I am not a python expert)
>>>  Anyway, at the moment the tutorial provides me enough stuff to 
>>> address my needs!
>>>  Once again, very thankful,for your hard work in making this code 
>>> available  and
>>> maintaining it!
>>>
>>> Thanks
>>> Raghvendra
>>>
>>> Sent from my iPad
>>>
>>> On Nov 17, 2015, at 7:26 AM, "Ken Dere" 
>>> <<mailto:kd...@gm...>kd...@gm...> wrote:
>>>
>>>> Hi Raghvendra,
>>>>
>>>> I am glad that you find ChiantiPy useful
>>>>
>>>> The quick start was the closes I have gotten to a manual. The 
>>>> CHIANTI group does have
>>>> a 'CHIANTI USERS GUIDE' on their website
>>>>
>>>> http://chiantidatabase.org
>>>>
>>>> this includes a lot of information but from an IDL perspective.
>>>
>>>
>>>>
>>>> The units for intensity are erg cm^-2 s^-1 sr^-1 / EM
>>>>
>>>> where EM = line of sight integral of n_e n_H dl
>>>>
>>>> there are not log files where errors are kept.  perhaps something 
>>>> for the future.
>>>>
>>>> also, I am confused by the chiantipy:discussion email address.  My 
>>>> emails seem to
>>>> bounce back from there
>>>>
>>>> best regards,
>>>>
>>>> Ken
>>>>
>>>> On 11/16/2015 05:30 PM, raghvendra sahai wrote:
>>>>>
>>>>> Hi Ken,
>>>>>
>>>>> i was able to get the ChiantiPy pacakge working on my office Linux 
>>>>> machine, and all
>>>>> the commands i've tried so far, from your tutorial page, have also 
>>>>> worked. i'm very
>>>>> excited how easy it is to use and I think this will be a great 
>>>>> tool for my research.
>>>>> Thanks very much for putting it together!
>>>>>
>>>>> is there a detailed manual for the full list of commands in 
>>>>> ChiantiPy, the syntax etc?
>>>>> i am sure i will have many more questions about using ChiantiPy, 
>>>>> and i would hate to
>>>>> pester you with these, if the information already can be gotten 
>>>>> from a manual! i know
>>>>> there is a chianti manual somwhe
>>>>>
>>>>> e.g., i'd like to know what the units of the intensities are, 
>>>>> e.g., when one makes a
>>>>> plot, with , e.g.,
>>>>> fe14.intensityPlot(wvlRange=[210.,220.],linLog='log')
>>>>>
>>>>> I read your reply to my query yesterday about my install on my 
>>>>> windows 8 laptop (but
>>>>> for some reason I can't [ or don't know how to] access your reply 
>>>>> again). Anyway, from
>>>>> what i recall, you suggested that the syntax I had used was 
>>>>> incorrect (it really
>>>>> wasn't, but doing cut-and-paste to put in the error text in my 
>>>>> email resulted in some
>>>>> funny chars).
>>>>> I tried again the commands again, just now, making sure that what 
>>>>> I am typing in,
>>>>> corresponds exactly to what is given in the tutorial, and I get 
>>>>> the same problem.
>>>>>
>>>>> even, the simple command
>>>>>
>>>>> fe14=ch.ion('fe_14') gives the same kind of problem ...
>>>>> TypeError: 'NoneType' object has no attribute '*getitem*'
>>>>>
>>>>> does ChiantiPy create an error log file that i can send you, so 
>>>>> you have the full
>>>>> output that appears on my terminal window and you can the more 
>>>>> easily see the problem?
>>>>>
>>>>> thanks much for your help
>>>>>
>>>>> raghvendra
>>>>>
>>>>> ------------------------------------------------------------------------------------------ 
>>>>>
>>>>>
>>>>> problem running commands from QuickStart webpage
>>>>> <https://sourceforge.net/p/chiantipy/discussion/907391/thread/0565ef6b/?limit=25#7fb2> 
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------------------ 
>>>>>
>>>>>
>>>>> Sent from sourceforge.net <http://sourceforge.net> because you 
>>>>> indicated interest in
>>>>> <https://sourceforge.net/p/chiantipy/discussion/907391/>https://sourceforge.net/p/chiantipy/discussion/907391/ 
>>>>>
>>>>>
>>>>> To unsubscribe from further messages, please visit
>>>>> <https://sourceforge.net/auth/subscriptions/>https://sourceforge.net/auth/subscriptions/ 
>>>>>
>>>>>
>>>>
>>>> -- 
>>>> Kenneth P. Dere
>>>> Research Professor of Solar Physics
>>>> Department of Computational and Data Sciences
>>>> George Mason University
>>>> kd...@gm...
>>>> ------------------------------------------------------------------------------ 
>>>>
>>>> _______________________________________________
>>>> Chiantipy-users mailing list
>>>> Chi...@li... 
>>>> <mailto:Chi...@li...>
>>>> https://lists.sourceforge.net/lists/listinfo/chiantipy-users
>>
>> -- 
>> Kenneth P. Dere
>> Research Professor of Solar Physics
>> Department of Computational and Data Sciences
>> George Mason University
>> kd...@gm...
>>
>

-- 
Kenneth P. Dere
Research Professor of Solar Physics
Department of Computational and Data Sciences
George Mason University
kd...@gm...