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Gammapy

A Python Package for Gamma-ray Astronomy.

Gammapy is an open-source Python package for gamma-ray astronomy built on Numpy, Scipy and Astropy. It is used as core library for the Science Analysis tools of the Cherenkov Telescope Array (CTA), recommended by the H.E.S.S. collaboration to be used for Science publications, and is already widely used in the analysis of existing gamma-ray instruments, such as MAGIC, VERITAS and HAWC.

Contributing Code, Documentation, or Feedback

The Gammapy Project is made both by and for its users, so we welcome and encourage contributions of many kinds. Our goal is to keep this a positive, inclusive, successful, and growing community by abiding with the Gammapy Community Code of Conduct.

The Gammapy project uses a mechanism known as a Developer Certificate of Origin (DCO). The DCO is a binding statement that asserts that you are the creator of your contribution, and that you wish to allow Gammapy to use your work to cite you as contributor. More detailed information on contributing to the project or submitting feedback can be found on the Contributing page.

Licence

Gammapy is licensed under a 3-clause BSD style license - see the LICENSE.rst file.

Supporting the project

The Gammapy project is not sponsored and the development is made by the staff of the institutes supporting the project over their research time. Any contribution is then encouraged, as punctual or regular contributor.

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gamma-sky's Issues

Load only relevant images into Aladin Lite dropdown

Most of the default images loaded by Aladin Lite in the dropdown tool are not relevant to us, and instead we want to add other high-energy images to the dropdown, like those from the Planck satellite.

There is no information on configuring the dropdown in the Aladin Lite docs. In order to figure it out ourselves, here are important lines in aladin.js:

AL map freezes during catalog load

I noticed that the Aladin Lite (AL) map freezes for a second while the Fermi catalog is loading.
@vorugantia - Can you try and play around with this and see if this can be avoided?

The goal is that the map is responsive ASAP and that other info, like this catalog, gets displayed whenever it arrives.

(I didn't look myself how the catalog loading works ... is A.catalogFromVizieR or aladin.addCatalog blocking? Is there a way to have it non-blocking?)

Introduce source class controls for catalogs

There's a lot of very bright sources on this low-energy Fermi-LAT images that we're currently using, that don't show up in the 2FHL catalog. Some of them are even blue, i.e. bright in the highest energy band on the image used.

I clicked on some of them, and as expected they are all pulsars (which have a steep cutoff in the spectrum).

It would be very nice to be able to select sources by souce type like at
http://fermi.gsfc.nasa.gov/ssc/data/access/lat/4yr_catalog/3FGL-table/#aitoff
or color the markers by source type.

This is just a reminder issue for this feature, I don't have specific suggestions yet for what exactly I would like to have or how it should be implemented.

screen shot 2016-07-09 at 01 10 58

Add information to TeV source detail page

In our old TeV catalog, we listed all extension, spectral, and distance info for each source's detailed view in CatViewComponent. @cdeil formatted the HTML in cat-source-tev.component.html and implemented getter methods in source.ts to do so.

However, our new TeV catalog organizes its data differently, in columns with new names, and I'm not sure how we would want to present the information in the detailed view. I will need some help doing this.

How to update dependencies?

After merging #30 in master and updating my master, the app doesn't start any more.
There's an error mentioning an issue with promises and zone.js in the console.

First thing I tried was npm install to update dependencies.
This fails with an install error mentioning also promises and zone.js:
https://gist.github.com/cdeil/114617b86c910a38eb61d59a532acc0c#file-gistfile1-txt-L1044

Next I did rm -r node_modes and a clean npm install and now ng serve works for me.

Arjun, could you please look around a bit what the normal update workflow is for node / Angular 2 projects and explain this with a sentence or two (and give the commands to run) in our developer docs?

We can practice this one more time. Currently we're on Angular RC 1.
@vorugantia - Please update to RC4:
http://angularjs.blogspot.de/2016/06/rc4-now-available.html
(I think all you have to do is run npm update commands or edit versions manually in package.json ... again, please figure out how this is properly done and document it in the developer documentation.)

I'm also getting this warning:

npm WARN deprecated [email protected]: Please update to minimatch 3.0.2 or higher to avoid a RegExp DoS issue

Is there a standard command / way to figure out which of our dependencies have updates, and to apply those updates?

From now on, all updates should go through pull requests, and the "version" in package.json which is currently at "0.0.0" should be increased every time.

Add SNRCat

@vorugantia - I know you're already working on adding SNRCat.

Let me know when it's deployed (or do a pull request if you prefer), and then I'll review and we can use this issue to discuss.

Control order of HiPS surveys in the image list

It would be good to be able to control the order of HiPS surveys in the image list.

Most important is Fermi-LAT above 10 GeV, which should be at the top and default.
Then others, maybe sorted by photon energy, i.e. radio at the bottom?

screen shot 2017-07-18 at 17 06 07

Load any image from HiPS database

For image selection in the Map View, we should probably find a way to load any HiPS image from the CDS database without having to define them all in surveys.ts like we currently are. We could then implement a ng2-select to go through the names of all the HiPS images from this database. This would give the user a much greater selection of maps.

Source search performance issues

I'm currently looking for the solution to loading 5000+ items in our search bar and getting very slow performance. Loading the search entries and typing in the search bar need to be asynchronous processes. A virtual/infinite scroll seems to be the solution (basically loading search results as you scroll down).

If I were to write up a virtual scroll myself, it would take about 500 lines (and lots of tricky code...) so it's probably more time-efficient to turn to a third-party npm package (a few of them exist.)

See this thread - Angular2 Material should be implementing a virtual scroll sometime later this year: This issue is a reminder to look into Material's version or virtual scroll when it's released.

3FHL sources show up with 2 different spectra

For 3FHL sources, the webpage shows two different sets of spectral parameters

See e.g. http://gamma-sky.net/#/cat/3fhl/0

Model Info

    Significance (10 GeV - 2 TeV): 5.362
    Npred: 7.63

    Spectrum type: PowerLaw
        Spectral index: 1.672 +/- 0.827
        Pivot energy: 23.7 GeV
        Flux density at pivot energy: 5.32e-13 +/- 2.10e-13 cm-2 s-1 GeV-1

    Power law index: 2.223 +/- 0.481
    Integral flux (10 GeV - 1 TeV): 2.96e-11 +/- 1.17e-11 cm-2 s-1
    Energy flux (10 GeV - 1 TeV): 1.68e-12 +/- 1.07e-12 erg cm-2 s-1
    Significance curvature: 1.02

If there is a good reason for that it should be explained somewhere, because the way it is right now might confuse people.

Configure base image layer options

Currently we have the following available images for the "base image layer":

screen shot 2016-07-07 at 20 52 11

These aren't the most interesting images to compare with the gamma-ray sky.
We should configure it to something better, more like http://www.chromoscope.net/

It looks like that list is defined here in the HpxImageSurvey.SURVEYS array:
https://github.com/gammapy/gamma-sky/blob/gh-pages/static/aladin.js#L8065

@vorugantia - Could you try modifying it? E.g. maybe it's possible to modify that array before calling the Aladin widget constructor?

A list of available HIPS images at CDS is available here:
http://aladin.u-strasbg.fr/hips/list

We want e.g. one from INTEGRAL:

But let's separate the discussion of which images to show from the question how to implement that selection, i.e. do the discussion elsewhere / later.

Map share URL

@vorugantia - I'm using the JS console at
http://aladin.u-strasbg.fr/AladinLite/doc/API/examples/AL-init-custom-options/
to play around with Aladin Lite a bit.

One method I noticed was this:

> aladin.getShareURL()
< "http://aladin.u-strasbg.fr/AladinLite/?target=06%2009%2039.000%2B20%2029%2012.12&fov=1.50&survey=P%2FallWISE%2Fcolor"

I'm not sure if / how we can use this for our app yet.
Maybe, as long as it's not connected to the router and app state, it could be exposed via a "share" button?

Implement some tests

Right now, the spec.ts files generated by angular-cli's ng generate are not running any useful tests. We want to implement unit tests on each component's and service's specific variables, routes, etc.

See these guides:

Download FITS images for given region

Feature request from Dirk Pandel at the Gamma 2016 poster -- for a given region, have a "download as FITS image" button.

I completely agree, I would use that as well.

It's not clear how to implement it, it might be very complicated and require lots of development effort in Aladin Lite in JS.
Maybe we could provide a Python script that takes a given view (encoded as a URL or JSON blob) and generates the FITS images.
This could then be exposed as a separate or built-in web service, or, for now, have to be run locally on their computer by the user.

Initial project setup

I think these are the main steps to set up the gamma-sky.net project in a good way:

  • Use https://cli.angular.io/ to set up a default project (doesn't have to contain a webpage yet). This should be done in the master branch and then the ng github-pages:deploy should deploy the app to the gh-pages branch.
  • Add a README.md with some info how the setup works and how to contribute
  • Set up automatic testing on https://travis-ci.org/ for the tests generated by the Angular cli
  • Add back the Python scripts and webpage that are currently here and make them work in the Angular webpage setup (probably can just put stuff in index.html for a start and refactor into components later

How to handle overlapping sources?

There's a few sources where we have multiple catalog entries.
E.g. the Crab has two 3FGL and one 2FHL entry that's almost at the same position.

One has to zoom in very far to see that there's multiple markers:

screen shot 2016-07-01 at 10 37 21

I'm not sure how to make this better ... I know that I've seen a d3 package that separates the points a little automatically when one hovers over them. Probably not easy to implement.

This is low priority, just a reminder issue.

Error loading data on source detail page from Angular Material searchbar

I've noticed this bug that sometimes appears when searching for and routing to a source (and it happens every time on my phone):

cat_error

I believe it has something to do with the code trying to fill in the HTML template with source data before the Http get request comes in. It may have to do specifically with the *ngIf method call in the HTML templates.

Appearance of website in Google search results

This is what the website currently looks like in Google search results:

search-result

See here for more information on what we can do to try and change the search results display. One thing we can do is call <meta name="nosnippets"> in index.html to completely remove the search results "snippet". But snippets are usually good, because more keywords will match from someone's Google search result and we may get more visibility.

@cdeil - Any ideas for what we can do?

Commit package-lock.json ?

@vorugantia - Should we commit package-lock.json?
I keep getting this warning:

$ npm install
npm notice created a lockfile as package-lock.json. You should commit this file.

and this file keeps getting generated and show up with git status:

$ git status
On branch master
Your branch is up-to-date with 'origin/master'.

Untracked files:
  (use "git add <file>..." to include in what will be committed)

	package-lock.json

nothing added to commit but untracked files present (use "git add" to track)

So we should either commit it, or add it to .gitignore.

@vorugantia - I think we should just commit it, no? If you have time, could you read around a bit how it's used (i.e. how one updates it as new versions of the dependencies pinned there appear), and add a link or two to a good reference to the gamma-sky.net dev docs?

Produce Fermi all-sky HEALPIX high-energy images

For the http://gamma-sky.net/ webpage we want to produce all-sky HEALPIX high-energy images.

We'll then convert those to http://aladin.u-strasbg.fr/hips/ and serve them as default image instead of the one from http://alasky.u-strasbg.fr/Fermi/Color/ which we use now.

My suggestion would be to make RGB images for the energy bands

  • R = 10 -- 30 GeV
  • G = 30 -- 100 GeV
  • B = 100 GeV -- 1 TeV

These are the energy bands I used many years ago (2011 I think) and the maps were interesting. See https://github.com/cdeil/fermi-ts-maps for Galactic plane images ... I also have old all-sky images in CAR and AIT, but I think we should just re-do them.

As for which quantity to show, my experience is that sqrt(TS) is good.
Other options would be smoothed counts or excess or flux.

Having catalog model images and residual images would also be very cool, to see where the catalog represents the data well and where it doesn't.

I don't have a working set of Python scripts any more to produce those TS images. So if someone else has them or is willing to write them and share scripts and / or maps, that would be great!

cc @woodmd @tburnett @dankocevski @adonath @vorugantia

About info should be visible on any page

Currently the "About" button is only visible on the maps page.
It would be good if on any page on gamma-sky.net there would be some way to reach this info.
Concretely on this page it's not clear how to find out what this webpage is: http://gamma-sky.net/#/cat/tev/142

@vorugantia - What do you think is the best (or quickest) way to improve this? Copy the "About" button onto that view? Or add a footer there, which just links to the docs, or shows the same popup?

On the desktop I like the buttons, but on my phone they are too large and don't work well as a user interface element. Not sure if we should put emphasis on mobile, just mentioning it. I think most people use it on their desktop / laptop, but I can imagine someone wants to quickly look up some source info on their phone during a presentation, so if it's possible to support, we should.

Add "version" and "last modified" to the "About" popup

I think we should have a version number (e.g. "version 0.1") and last modified date stamp (e.g. "July 7, 2016") in the "About" popup on the webpage.

This will be useful for us to see which version is deployed, but also for users.

A nice way to implement it is to store those pieces of info in a separate hand-written file gamma-sky.info.json.
That way it's under version control, and accessible both from Python and JS scripts.
(Although for now we'll just access it from JS to display on the webpage)

Add GLEAM images

I just now saw the GLEAM survey images here:
http://www.nature.com/news/gleam-highres-composite-jpg-7.41222?article=1.21156

Looking here, it seems that they have nice images of some supernova remnants and other Galactic emission components (scroll down to the GLEAM wavelength):
http://gleamoscope.icrar.org/gleamoscope/trunk/src/

There's descriptions here:
http://www.mwatelescope.org/science/gleam-survey
https://arxiv.org/pdf/1505.06041v1.pdf
but I didn't see FITS images or a HIPS version here yet:
http://aladin.u-strasbg.fr/hips/list

When a HIPS version is available, we should add it to gamma-sky.net

Catalog data panel

It would be nice to have a "data panel" at the side (example: http://sky.esa.int/ has a data panel at the bottom) that displays some catalog data as a table (example: http://gammapy.github.io/web-experiments/?cat=2FHL&source=2) when I click on a given source.

I like the idea of starting with almost 100% of the space for the map, and then to only reduce screen space for the map when the user asks for it, but shrinking the map or painting information or panels on top.

FYI: I'll just start filing some feature requests for the webpage when I think of something.
Some of them are easy to implement, others a week of work.

As far as I'm concerned, you already have built version 0.1 and it's good enough for now.
So feel free to just pick whatever you find interesting and work on that on hour own time.

Bug when clicking on SNRcat source

Every time I click on an SNRcat source in MapView, all of the text in the toolbox and the about button text gets aligned to the right. See before and after pics below.

snrcat_bug2

snrcat_bug

It's probably an easy fix and I'll just do it later. This is just a reminder for myself

Search prompt does work with 'common name'

The search prompt in the catalog view of gamma-sky.net only works with the common name of a source.

For example if I want the VHE Energy source at the GC, I have to type 'Galactic Center', 'HESS J1745-290' does not work. This is confusing, because for other sources (e.g. HESS J1745-303) the "HESS name" is the common name so when I start typing 'HESS J...' I do get suggestions, they just don't contain the source I'm looking for (HESS J1745-290).

I would suggest to also prompt Gamma names, Fermi names, and other names in the search prompt, unless there is a technical reason not to do so.

CSS styles

Concerning yesterday’s discussion how to avoid duplication of css style code.

There’s a very simple solution … every component can have a list of styles from multiple css files applied by listing those files in styleUrls:

https://angular.io/docs/ts/latest/guide/component-styles.html#!#loading-styles

So every time we have shared styles, we can just add those in css files that are then applied to multiple components.
E.g. we could start with one such global style that defines the fonts and gets applied to all components that show text.

Probably we should use a CSS framework to get nice styling with little work.
I'm only familiar with bootstrap, so that would be my preference.
I've never used it in combination with Angular 2 though.

Looks like this is the most popular option:
https://github.com/valor-software/ng2-bootstrap

And this one is also popular:
https://github.com/ng-bootstrap/ng-bootstrap

There's also material design:
https://github.com/angular/material2
but it's very early in development, I'm not sure if it would work for us yet.

In any case: let's talk about styling next week, let's first get the app functional.

List of interesting objects / regions

We should have a curated list of interesting objects or regions.

For now it could just be a list of source names in the docs, e.g.

  • Crab nebula
  • Galactic center
  • Vela pulsar

Then later once we have a router these should be links to that view.

And even later, we could have a "guided tour" like http://www.worldwidetelescope.org/ for certain sub-classes of gamma-ray sources (e.g. pulsars, SNRs, AGN, ...) or regions (e.g. Galactic center, Vela region, Cygnus region) that are interesting.

But I think maybe starting a "tutorial" or "getting started" in the docs with just some instructions what to try could be a good first step.

Improvement for http://gamma-sky.net/

@vorugantia - I suggest the following changes to http://gamma-sky.net/

  • For me, the canvas doesn't fill the browser window exactly. There's some small space on the top and left that's unused, and some of the canvas at the right and bottom is cut off in Chrome. Do you see the same? Can you try to fix it?
  • Change default image to Fermi color
  • Change default coordinate system from ICRS to Galactic
  • Default position = Galactic center
  • Load full Fermi 3FGL catalog

gamma-sky.net and gamma-cat logos

@vorugantia - I wanted to ask you if you'd be interested in making a logo and banner for gamma-sky.net, and maybe also for gamma-cat?

If you don't have time or aren't interested, I can do this in the coming days.

My idea would be that we do something similar like I did for Gammapy:

Overall it's quite a bit of work to do it will, i.e. to have PDF and PNG versions (and possibly also SVG), and to have a logo and a banner. See:
https://github.com/gammapy/gammapy-extra/tree/master/logo


For gamma-sky.net, my suggestion would be that as logo we do some sphere (e.g. grid lines or stylised in some other ways). It must be very simple so that it works as a logo. Examples (probably can't be taken for copyright reasons, must be re-drawn):
https://www.google.com/search?q=sphere+symbol&espv=2&biw=1440&bih=748&source=lnms&tbm=isch&sa=X&ved=0ahUKEwiGqZLLtNvRAhVsAcAKHaA8BuMQ_AUIBigB

Then for the banner, we would put "gamma-sky.net" in large font, and "Portal to the gamma-ray sky" or "A portal to the gamma-ray sky", which we already discussed and chose as our slogan or tagline.

For gamma-cat, I'm not sure what symbol to put. The tagline is "An open data collection and source catalog for gamma-ray astronomy" at the moment, which is a bit long to fit. Maybe change to "Open gamma-ray data archive" or "The open gamma-ray data archive"?

Colors could all be matching the grey and red from Gammapy, so that the three together form a brand:

  • gammapy: analysis
  • gamma-cat: data archive
  • gamma-sky.net: portal

Maybe I should buy "gamma-cat.net" or "gamma-cat.org" now, so that we have a permanent and nice and simple URL for the coming years?

@adonath @joleroi - Thoughts?

Add router

It would be nice to be able to "share" a given view / state of gamma-sky.new with others.
The easiest way would be if we have a router and the state of the app (or part of it, like the map position and zoom level) could be encoded in the URL.

Examples:
http://gammapy.github.io/web-experiments/?cat=2FHL&source=2
http://aladin.u-strasbg.fr/AladinLite/?target=&fov=3.00&survey=P%2FFermi%2Fcolor
https://www.google.com/maps/place/Max+Planck+Institute+for+Nuclear+Physics/@49.38803,8.7073313,17z/data=!3m1!4b1!4m5!3m4!1s0x4797c05ed0bff2df:0x278a1dd9700fcbf7!8m2!3d49.38803!4d8.70952

I think this is something that's a lot of work to implement and maybe it would be best to go to Angular 2 first?
https://angular.io/docs/ts/latest/guide/router.html
https://angular.io/docs/ts/latest/tutorial/toh-pt5.html
http://blog.thoughtram.io/angular/2016/06/14/routing-in-angular-2-revisited.html
The alternative would be that for now we add some other small router like
https://github.com/flatiron/director
(I haven't used either and don't know much about how they work ... we can work on this together next week.)

Add TeGeV catalog

I've found this catalog of TeV sources: http://www.asdc.asi.it/tgevcat/

I don't know how good it is or if it's maintained.
But there's a CSV download option and maybe one can even get it as a VOTable?

I think for now we could use it for gamma-sky.net .

Tasks:

Add spectrum and lightcurve for 3FGL

@dankocevski has produced PNG images for spectrum / lightcurve fore every 3FGL source for this webpage:
http://fermi.gsfc.nasa.gov/ssc/data/access/lat/4yr_catalog/3FGL-table/#aitoff

Example:
http://fermi.gsfc.nasa.gov/ssc/data/access/lat/4yr_catalog/3FGL-table/data/3FGL_lc_v5/3FGL_J0002d6p6218_lc.png

They can be accessed from the popup:
screen shot 2016-07-07 at 21 11 33

Eventually we want to generate our own images or have a JS visualisation of 3FGL and 2FHL and other spectra and images, but for now we don't have this ready.

@dankocevski - Would it be OK if we link to your PNGs for now?

Update to Angular 2 final

Angular 2 final was realeased:
http://angularjs.blogspot.de/2016/09/angular2-final.html

We are currently on 2.0.0-rc.4 and should update.

I'm not sure how to best do the update yet.

I guess roughly the options are:

  1. use the CLI to make a new project to get a cleanly set up and working project following latest best practices, then copy over existing code piece by piece.
  2. make changes to the current app, after reading through the RC4 to RC5 migration guide.

@vorugantia - Any idea which might be better? Will you have time for this in the coming weeks or should I give it a go?

Change styling to Angular Material

Our current styling tools (Boostrap 3, ng2-select, etc.) are outdated and also not optimized for Angular. Although they still work fine, this would be the better alternative moving forward:

https://material.angular.io/

It's not a high-priority change, but eventually it would be nice to change to Angular Material for styling.

Behaviour for invalid routes

I tried some invalid routes.

E.g. http://localhost:4200/spam results in a white screen and a JS error in the console.

E.g. http://localhost:4200/cat/tev/999 results in an empty source detail view.

@vorugantia - Can we do better?

I think a 404 "not found" page is pretty standard and shouldn't be hard to implement in the router?
(see https://github.com/spam/spam for an example)
Or maybe it is hard to implement for the source detail views where you have to check if the source_id exists?

Which catalog markers to show on page load?

Currently, Aladin Lite is showing all catalog markers by default on the map, which is getting a little cluttered:

capture

However, now (thanks to Thomas Boch) I found the workaround to hide certain catalogs on page load (while still keeping the check-box in the toolbar to re-enable them). @cdeil - which catalogs should we hide on page load? I think since 3FGL has the most sources by far, if we were to hide them, the map would look much cleaner on startup.

This is a low priority question, we can decide later.

Credits

Before Gamma 2016 we should add a section where we give credit to people and projects that have helped create gamma-sky.

Here's the start of an incomplete list:

I'm not sure where this fits on the webpage.
Maybe we can just have a Markdown file in the repo and link to it from the webpage?

Start an open TeV source catalog?

We've been discussing the option of starting our own TeV source catalog because http://tevcat.uchicago.edu/ is not really open. They don't provide the option to download the catalog and from private communication I know that they don't want people to use the full TeV catalog data as they like, like in our case display it as part of the available info on gamma-sky.net .

When I thought about how to implement it, I was thinking about storing the data in YAML files in a Github repo, so that it's easy to edit and maintain and accept issues and PRs from the community. Just now I found https://github.com/astrocatalogs/astrocats where others have done such "open catalogs" using JSON files in Github repos and have even developed some tooling to process it and make webpages to view / browse the data and click "edit".

So I guess we should follow through with this idea and make an open TeV source catalog either at https://github.com/astrocatalogs/ or at https://github.com/gammapy/ . Ideally this effort would merge with TeVCat at some point in the future, if they change their mind and make the catalog fully open.

This is just a reminder issue. Not high priority. I won't have time for this before going on holiday.

Related: #22

Update typescript

I'm deploying a new version just now.

One error I'm getting is this:

$ ng build --target=production --aot=false --base-href ./

@angular/[email protected] requires typescript@'>=2.1.0 <2.4.0' but 2.5.2 was found instead.
Using this version can result in undefined behaviour and difficult to debug problems.

Please run the following command to install a compatible version of TypeScript.

    npm install typescript@'>=2.1.0 <2.4.0'

To disable this warning run "ng set --global warnings.typescriptMismatch=false".

@vorugantia - Can you please try to upgrade (maybe in the same PR where you add the package-lock.json? Maybe it would be useful to add this production build command on travis-ci at the end?

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