def test_getFullPath_no_plateifu(self, galaxy):
cube = Cube(mangaid=galaxy.mangaid)
cube.plateifu = None
assert cube._getFullPath() is None
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']
self.galaxy['latest_dr'] = self._release.lower() if 'DR' in self._release else marvin.config._get_latest_release(dr_only=True).lower()
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
errmsg = 'MarvinError: {0}'.format(e)
# check target status and fine-tune the error message
if idtype == 'mangaid':
status = target_status(galid, drpver=self._drpver)
if status == 'not yet observed':
errmsg = '{0} is a valid target but has not yet been observed'.format(galid)
elif status == 'not valid target':
errmsg = '{0} is not valid MaNGA target. Check your syntax'.format(galid)
self.galaxy['error'] = errmsg
return render_template("galaxy.html", **self.galaxy)
else:
dm = datamodel[self._dapver]
self.galaxy['cube'] = cube
g.cube = cube
self.galaxy['daplink'] = getDapRedux(release=self._release)
# get SAS url links to cube, rss, maps, image
if Path:
sdss_path = Path(release=self._release)
self.galaxy['image'] = cube.getImage().url
cubelink = sdss_path.url('', full=cube._getFullPath())
rsslink = sdss_path.url('mangarss', drpver=cube._drpver, plate=cube.plate, ifu=cube.ifu, wave='LOG')
daptype = "{0}-{1}".format(dm.default_bintype, dm.default_template)
maplink = getDefaultMapPath(release=self._release, plate=cube.plate, ifu=cube.ifu, daptype=daptype, mode='MAPS')
mclink = getDefaultMapPath(release=self._release, plate=cube.plate, ifu=cube.ifu, daptype=daptype, mode='LOGCUBE')
self.galaxy['links'] = {'cube': cubelink, 'rss': rsslink, 'map': maplink, 'mc': mclink}
else:
self.galaxy['image'] = cube.data.image
infile = get_manga_image(cube, local=True)
current_session['imagefile'] = infile
current_session['wcs'] = cube.wcs.to_header_string()
current_session['cube_shape'] = cube.wcs.array_shape[-1]
# Get the initial spectrum
if cube:
dm = datamodel[self._dapver]
daplist = [p.full(web=True) for p in dm.properties]
dapdefaults = dm.get_default_mapset()
self.galaxy['cube'] = cube
self.galaxy['toggleon'] = current_session.get('toggleon', 'false')
self.galaxy['cubehdr'] = cube.header
self.galaxy['quality'] = ('DRP3QUAL', cube.quality_flag.mask, cube.quality_flag.labels)
self.galaxy['mngtarget'] = {'bits': [it.mask for it in cube.target_flags if it.mask != 0],
'labels': [it.labels for it in cube.target_flags if len(it.labels) > 0],
'names': [''.join(('MNGTARG', it.name[-1])) for it in cube.target_flags if it.mask != 0]}
# 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 if i in nsacols]
nsatmp.extend(nsacols)
self.galaxy['nsacols'] = nsatmp
self.galaxy['nsadict'] = nsadict
self.galaxy['dapmaps'] = daplist
self.galaxy['dapmapselect'] = current_session.get('selected_dapmaps', dapdefaults)
dm = datamodel[self._dapver]
self.galaxy['dapbintemps'] = dm.get_bintemps(db_only=True)
if 'bintemp' not in current_session or current_session['bintemp'] not in self.galaxy['dapbintemps']:
current_session['bintemp'] = '{0}-{1}'.format(dm.get_bintype(), dm.get_template())
# get default map quality
try:
maps = cube.getMaps(plateifu=cube.plateifu, mode='local', bintype=current_session['bintemp'].split('-')[0])
except MarvinError:
mapqual = ('DAPQUAL', [], [])
else:
mapqual = ('DAPQUAL', maps.quality_flag.mask, maps.quality_flag.labels)
self.galaxy['mapquality'] = mapqual
# 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 by slicing cube[i,j]<br>spaxel=cube[16, 16]<br>flux = \
spaxel.flux<br>wave = flux.wavelength<br>ivar = flux.ivar<br>mask = \
flux.mask<br>flux.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.emline_gflux_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)
