def set_filenames(self, bintype=None, template=None):
default_bintemp = _get_bintemps(self.dapver, default=True)
default_bin, default_temp = default_bintemp.split('-', 1)
self.bintype = bintype if bintype is not None else default_bin
self.template = template if template is not None else default_temp
self.bintemp = '{0}-{1}'.format(self.bintype, self.template)
self.cubename = 'manga-{0}-LOGCUBE.fits.gz'.format(self.plateifu)
self.rssname = 'manga-{0}-LOGRSS.fits.gz'.format(self.plateifu)
self.imgname = '{0}.png'.format(self.ifu)
self.mapsname = 'manga-{0}-MAPS-{1}.fits.gz'.format(
self.plateifu, self.bintemp)
self.modelname = 'manga-{0}-LOGCUBE-{1}.fits.gz'.format(
self.plateifu, self.bintemp)
def setUpClass(cls):
config.use_sentry = False
config.add_github_message = False
# set initial config variables
cls.init_mode = config.mode
cls.init_sasurl = config.sasurl
cls.init_urlmap = config.urlmap
cls.init_xyorig = config.xyorig
cls.init_traceback = config._traceback
cls.init_keys = ['mode', 'sasurl', 'urlmap', 'xyorig', 'traceback']
# set db stuff
cls._marvindb = marvindb
cls.session = marvindb.session
# set paths
cls.sasbasedir = os.getenv("$SAS_BASE_DIR")
cls.mangaredux = os.getenv("MANGA_SPECTRO_REDUX")
cls.mangaanalysis = os.getenv("MANGA_SPECTRO_ANALYSIS")
# testing data for 8485-1901
cls.set_plateifu(plateifu='8485-1901')
cls.mangaid = '1-209232'
cls.cubepk = 10179
cls.ra = 232.544703894
cls.dec = 48.6902009334
cls.redshift = 0.0407447
cls.dir3d = 'stack'
cls.release = 'MPL-5'
cls.drpver, cls.dapver = config.lookUpVersions(cls.release)
cls.bintemp = _get_bintemps(cls.dapver, default=True)
cls.defaultbin, cls.defaulttemp = cls.bintemp.split('-', 1)
cls.cubename = 'manga-{0}-LOGCUBE.fits.gz'.format(cls.plateifu)
cls.rssname = 'manga-{0}-LOGRSS.fits.gz'.format(cls.plateifu)
cls.imgname = '{0}.png'.format(cls.ifu)
cls.mapsname = 'manga-{0}-MAPS-{1}.fits.gz'.format(cls.plateifu, cls.bintemp)
cls.modelname = 'manga-{0}-LOGCUBE-{1}.fits.gz'.format(cls.plateifu, cls.bintemp)
def initDynamic(self):
''' Route to run when the dynamic toggle is initialized
This creates the web spectrum and dap heatmaps
'''
# get the form parameters
args = av.manual_parse(self,
request,
use_params='galaxy',
required='plateifu')
#self._drpver, self._dapver, self._release = parseSession()
# turning toggle on
current_session['toggleon'] = args.get('toggleon')
# get the cube
cubeinputs = {
'plateifu': args.get('plateifu'),
'release': self._release
}
cube = Cube(**cubeinputs)
output = {'specstatus': -1, 'mapstatus': -1}
# get web spectrum
webspec, specmsg = getWebSpectrum(cube,
cube.ra,
cube.dec,
byradec=True)
daplist = get_dap_maplist(self._dapver, web=True)
dapdefaults = get_default_mapset(self._dapver)
# build the uber map dictionary
try:
mapdict = buildMapDict(cube, dapdefaults, self._dapver)
mapmsg = None
except Exception as e:
mapdict = [{
'data': None,
'msg': 'Error',
'plotparams': None
} for m in dapdefaults]
mapmsg = 'Error getting maps: {0}'.format(e)
else:
output['mapstatus'] = 1
if not webspec:
output['error'] = 'Error: {0}'.format(specmsg)
else:
output['specstatus'] = 1
sdss_path = Path()
output['image'] = sdss_path.url('mangaimage',
drpver=cube._drpver,
plate=cube.plate,
ifu=cube.ifu,
dir3d=cube.dir3d)
output['spectra'] = webspec
output['specmsg'] = specmsg
output['maps'] = mapdict
output['mapmsg'] = mapmsg
output['dapmaps'] = daplist
output['dapbintemps'] = _get_bintemps(self._dapver)
current_session['bintemp'] = '{0}-{1}'.format(
_get_bintype(self._dapver), _get_template_kin(self._dapver))
return jsonify(result=output)
def get(self, galid):
''' Retrieve info for a given cube '''
# determine type of galid
args = av.manual_parse(self, request, use_params='galaxy')
self.galaxy['id'] = args['galid']
idtype = parseIdentifier(galid)
if idtype in ['plateifu', 'mangaid']:
# set plateifu or mangaid
self.galaxy['idtype'] = idtype
galaxyid = {self.galaxy['idtype']: galid, 'release': self._release}
# Get cube
try:
cube = Cube(**galaxyid)
except MarvinError as e:
self.galaxy['cube'] = None
self.galaxy['error'] = 'MarvinError: {0}'.format(e)
return render_template("galaxy.html", **self.galaxy)
else:
self.galaxy['cube'] = cube
self.galaxy['daplink'] = getDapRedux(release=self._release)
# get SAS url links to cube, rss, maps, image
if Path:
sdss_path = Path()
self.galaxy['image'] = sdss_path.url('mangaimage',
drpver=cube._drpver,
plate=cube.plate,
ifu=cube.ifu,
dir3d=cube.dir3d)
cubelink = sdss_path.url('mangacube',
drpver=cube._drpver,
plate=cube.plate,
ifu=cube.ifu)
rsslink = sdss_path.url('mangarss',
drpver=cube._drpver,
plate=cube.plate,
ifu=cube.ifu)
maplink = getDefaultMapPath(release=self._release,
plate=cube.plate,
ifu=cube.ifu,
daptype='SPX-GAU-MILESHC',
mode='MAPS')
self.galaxy['links'] = {
'cube': cubelink,
'rss': rsslink,
'map': maplink
}
else:
self.galaxy['image'] = cube.data.image
# Get the initial spectrum
if cube:
daplist = get_dap_maplist(self._dapver, web=True)
self.galaxy['cube'] = cube
self.galaxy['toggleon'] = current_session.get(
'toggleon', 'false')
self.galaxy['cubehdr'] = cube.header
self.galaxy['quality'] = cube.qualitybit
self.galaxy['mngtarget'] = cube.targetbit
# make the nsa dictionary
hasnsa = cube.nsa is not None
self.galaxy['hasnsa'] = hasnsa
if hasnsa:
cols = self.galaxy.get('nsaplotcols')
nsadict, nsacols = make_nsa_dict(cube.nsa)
nsatmp = [nsacols.pop(nsacols.index(i)) for i in cols]
nsatmp.extend(nsacols)
self.galaxy['nsacols'] = nsatmp
self.galaxy['nsadict'] = nsadict
self.galaxy['dapmaps'] = daplist
self.galaxy['dapbintemps'] = _get_bintemps(self._dapver)
current_session['bintemp'] = '{0}-{1}'.format(
_get_bintype(self._dapver),
_get_template_kin(self._dapver))
# TODO - make this general - see also search.py for querystr
self.galaxy['cubestr'] = (
"<html><samp>from marvin.tools.cube import Cube<br>cube = \
Cube(plateifu='{0}')<br># access the header<br>cube.header<br># get NSA data<br>\
cube.nsa<br></samp></html>".format(cube.plateifu))
self.galaxy['spaxelstr'] = (
"<html><samp>from marvin.tools.cube import Cube<br>cube = \
Cube(plateifu='{0}')<br># get a spaxel<br>spaxel=cube[16, 16]<br>spec = \
spaxel.spectrum<br>wave = spectrum.wavelength<br>flux = spectrum.flux<br>ivar = \
spectrum.ivar<br>mask = spectrum.mask<br>spec.plot()<br></samp></html>"
.format(cube.plateifu))
self.galaxy['mapstr'] = (
"<html><samp>from marvin.tools.maps import Maps<br>maps = \
Maps(plateifu='{0}')<br>print(maps)<br># get an emission \
line map<br>haflux = maps.getMap('emline_gflux', channel='ha_6564')<br>values = \
haflux.value<br>ivar = haflux.ivar<br>mask = haflux.mask<br>haflux.plot()<br>\
</samp></html>".format(cube.plateifu))
else:
self.galaxy[
'error'] = 'Error: Galaxy ID {0} must either be a Plate-IFU, or MaNGA-Id designation.'.format(
galid)
return render_template("galaxy.html", **self.galaxy)
return render_template("galaxy.html", **self.galaxy)
from marvin.tools.maps import _get_bintemps
# class MarvinTest
# TODO Replace skipTest and skipBrian with skipif
# TODO use monkeypatch to set initial config variables
# TODO replace _reset_the_config with monkeypatch
# TODO reimplement set_sasurl (use function-level fixture?)
releases = ['MPL-4', 'MPL-5']
plateifus = ['8485-1901']
bintypes = {}
for release in releases:
__, dapver = config.lookUpVersions(release)
bintypes[release] = [
bintemp.split('-')[0] for bintemp in _get_bintemps(dapver)
]
class Galaxy:
"""An example galaxy for Marvin-tools testing."""
sasbasedir = os.getenv("$SAS_BASE_DIR")
mangaredux = os.getenv("MANGA_SPECTRO_REDUX")
mangaanalysis = os.getenv("MANGA_SPECTRO_ANALYSIS")
dir3d = 'stack'
def __init__(self, plateifu):
self.plateifu = plateifu
self.plate, self.ifu = self.plateifu.split('-')
self.plate = int(self.plate)
def _get_bin_temps(self):
''' Gets the bintemps for a given release '''
bintemps = _get_bintemps(self.dapver)
return bintemps