def test_public(self):
path = Path()
url = path.url('mangacube', drpver='v2_3_1', plate=8485, ifu='1901')
assert 'mangawork' in url
release = 'dr14'
path = Path(public=True, release=release)
url = path.url('mangacube', drpver='v2_3_1', plate=8485, ifu='1901')
assert release in url
def _getFullPath(self, pathType=None, url=None, **pathParams):
"""Returns the full path of the file in the tree.
This method must be overridden by each subclass.
"""
# # check for public release
# is_public = 'DR' in self._release
# ismpl = 'MPL' in self._release
# path_release = self._release.lower() if is_public or ismpl else None
if not Path:
raise MarvinMissingDependency('sdss_access is not installed')
else:
path = Path(release=self._release)
try:
if url:
fullpath = path.url(pathType, **pathParams)
else:
fullpath = path.full(pathType, **pathParams)
except Exception as ee:
warnings.warn(
'sdss_access was not able to retrieve the full path of the file. '
'Error message is: {0}'.format(str(ee)), MarvinUserWarning)
fullpath = None
return fullpath
def getDapRedux(release=None):
''' Retrieve SAS url link to the DAP redux directory
Parameters:
release (str):
The release version of the data to download.
Defaults to Marvin config.release.
Returns:
dapredux (str):
The full redux path to the DAP MAPS
'''
if not Path:
raise MarvinError('sdss_access is not installed')
else:
sdss_path = Path()
release = release or marvin.config.release
drpver, dapver = marvin.config.lookUpVersions(release=release)
# hack a url version of MANGA_SPECTRO_ANALYSIS
dapdefault = sdss_path.dir('mangadefault',
drpver=drpver,
dapver=dapver,
plate=None,
ifu=None)
dappath = dapdefault.rsplit('/', 2)[0]
dapredux = sdss_path.url('', full=dappath)
return dapredux
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')
# 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['dapmapselect'] = dapdefaults
dm = datamodel[self._dapver]
output['dapbintemps'] = dm.get_bintemps(db_only=True)
current_session['bintemp'] = '{0}-{1}'.format(dm.get_bintype(), dm.get_template())
# try to jsonify the result
try:
jsonout = jsonify(result=output)
except Exception as e:
jsonout = jsonify(result={'specstatus': -1, 'mapstatus': -1, 'error': '{0}'.format(e)})
return jsonout
def getDefaultMapPath(**kwargs):
''' Retrieve the default Maps path
Uses sdss_access Path to generate a url download link to the
default MAPS file for a given MPL.
Parameters:
release (str):
The release version of the data to download.
Defaults to Marvin config.release.
plate (int):
The plate id
ifu (int):
The ifu number
bintype (str):
The bintype of the default file to grab. Defaults to MAPS
daptype (str):
The daptype of the default map to grab. Defaults to SPX-MILESHC
Returns:
maplink (str):
The sas url to download the default maps file
'''
if not Path:
raise MarvinError('sdss_access is not installed')
else:
sdss_path = Path()
# Get kwargs
release = kwargs.get('release', marvin.config.release)
drpver, dapver = marvin.config.lookUpVersions(release=release)
plate = kwargs.get('plate', None)
ifu = kwargs.get('ifu', None)
daptype = kwargs.get('daptype', 'SPX-GAU-MILESHC')
bintype = kwargs.get('bintype', 'MAPS')
# get the sdss_path name by MPL
# TODO: this is likely to break in future MPL/DRs. Just a heads up.
if '4' in release:
name = 'mangadefault'
elif '5' in release:
name = 'mangadap5'
else:
return None
# construct the url link to default maps file
maplink = sdss_path.url(name,
drpver=drpver,
dapver=dapver,
mpl=release,
plate=plate,
ifu=ifu,
daptype=daptype,
mode=bintype)
return maplink
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
p = Path()
self.template = p.templates[self.name]
if self.kwargs:
self.full = p.full(self.name, **self.kwargs)
self.url = p.url(self.name, **self.kwargs)
self.file = p.name(self.name, **self.kwargs)
self.location = p.location(self.name, **self.kwargs)
self.exists = p.exists(self.name, **self.kwargs)
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)
dapdefaults = get_default_mapset(self._dapver)
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]
nsatmp.extend(nsacols)
self.galaxy['nsacols'] = nsatmp
self.galaxy['nsadict'] = nsadict
self.galaxy['dapmaps'] = daplist
self.galaxy['dapmapselect'] = dapdefaults
dm = datamodel[self._dapver]
self.galaxy['dapbintemps'] = dm.get_bintemps(db_only=True)
current_session['bintemp'] = '{0}-{1}'.format(dm.get_bintype(), dm.get_template())
# 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>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)
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
self.galaxy['daplink'] = getDapRedux(release=self._release)
# get SAS url links to cube, rss, maps, image
if Path:
is_public = 'DR' in self._release
path_release = self._release.lower() if is_public else None
sdss_path = Path(public=is_public, release=path_release)
self.galaxy['image'] = cube.getImage().url
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)
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
# 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
maps = cube.getMaps(
plateifu=cube.plateifu,
mode='local',
bintype=current_session['bintemp'].split('-')[0])
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)