def updateMaps(self):
args = av.manual_parse(self, request, use_params='galaxy', required=['plateifu', 'bintemp', 'params[]'], makemulti=True)
#self._drpver, self._dapver, self._release = parseSession()
cubeinputs = {'plateifu': args.get('plateifu'), 'release': self._release}
params = args.getlist('params[]', type=str)
bintemp = args.get('bintemp', None, type=str)
current_session['bintemp'] = bintemp
# get cube (self.galaxy['cube'] does not work)
try:
cube = Cube(**cubeinputs)
except Exception as e:
cube = None
# Try to make the web maps
if not cube:
output = {'mapmsg': 'No cube found', 'maps': None, 'status': -1}
elif not params:
output = {'mapmsg': 'No parameters selected', 'maps': None, 'status': -1}
else:
try:
mapdict = buildMapDict(cube, params, self._dapver, bintemp=bintemp)
except Exception as e:
output = {'mapmsg': e.message, 'status': -1, 'maps': None}
else:
output = {'mapmsg': None, 'status': 1, 'maps': mapdict}
return jsonify(result=output)
def galaxy_get_cache(*args, **kwargs):
''' Function used to generate the route cache key
Cache key when using cache.memoize or cache.cached decorator.
memoize remembers input methods arguments; cached does not.
Parameters:
args (list):
a list of the fx/method route call and object instance (self)
kwargs (dict):
a dictonary of arguments passed into the method
Returns:
A string used for the cache key lookup
'''
# get the method and self instance
fxn, inst = args
# parse the form request to extract any parameters
reqargs = av.manual_parse(inst, request, use_params='galaxy')
galid = reqargs.get('galid').replace('-', '_')
release = inst._release.lower().replace('-', '')
# create unique cache key name
key = 'getpage_{0}_{1}'.format(release, galid)
# append if logged in
if inst.galaxy['loggedin']:
key = '{0}_loggedin'.format(key)
return key
def update_maps_cache(*args, **kwargs):
''' Function used to generate the route cache key
Cache key when using cache.memoize or cache.cached decorator.
memoize remembers input methods arguments; cached does not.
Parameters:
args (list):
a list of the fx/method route call and object instance (self)
kwargs (dict):
a dictonary of arguments passed into the method
Returns:
A string used for the cache key lookup
'''
# get the method and self instance
fxn, inst = args
# parse the form request to extract any parameters
reqargs = av.manual_parse(inst, request, use_params='galaxy', required=[
'plateifu', 'bintemp', 'params[]'], makemulti=True)
plateifu = reqargs.get('plateifu').replace('-', '_')
release = inst._release.lower().replace('-', '')
bintemp = reqargs.get('bintemp', None, type=str).replace('-', '_')
params = reqargs.getlist('params[]', type=str)
params.sort()
param_string = '_'.join(params).replace(':', '_')
# create unique cache key name
key = 'updatemaps_{0}_{1}_{2}_{3}'.format(release, plateifu, bintemp, param_string)
return key
def getSpaxel(self):
args = av.manual_parse(self, request, use_params='galaxy', required=['plateifu', 'type'], makemulti=True)
cubeinputs = {'plateifu': args.get('plateifu'), 'release': self._release}
maptype = args.get('type', None)
if maptype == 'optical':
# for now, do this, but TODO - general processRequest to handle lists and not lists
try:
mousecoords = args.getlist('mousecoords[]', type=float)
except Exception as e:
mousecoords = None
if mousecoords:
pixshape = (args.get('imwidth', type=int), args.get('imheight', type=int))
if (mousecoords[0] < 0 or mousecoords[0] > pixshape[0]) or (mousecoords[1] < 0 or mousecoords[1] > pixshape[1]):
output = {'specmsg': 'Error: requested pixel coords are outside the image range.', 'status': -1}
self.galaxy['error'] = output['specmsg']
else:
cube = Cube(**cubeinputs)
# TODO - generalize image file sas_url to filesystem switch, maybe in sdss_access
infile = get_manga_image(cube, local=True)
current_session['imagefile'] = infile
#infile = os.path.join(os.getenv('MANGA_SPECTRO_REDUX'), args.get('image').split('redux/')[1])
arrcoords = convertImgCoords(mousecoords, infile, to_radec=True)
webspec, specmsg, badspots = getWebSpectrum(cube, arrcoords[0], arrcoords[1], byradec=True)
if not webspec:
self.galaxy['error'] = 'Error: {0}'.format(specmsg)
status = -1
else:
status = 1
msg = 'gettin some spaxel at RA/Dec {0}'.format(arrcoords)
output = {'message': msg, 'specmsg': specmsg, 'spectra': webspec, 'status': status, 'badspots': badspots}
else:
output = {'specmsg': 'Error getting mouse coords', 'status': -1}
self.galaxy['error'] = output['specmsg']
elif maptype == 'heatmap':
# grab spectrum based on (x, y) coordinates
x = args.get('x', None, type=int)
y = args.get('y', None, type=int)
if all([x, y]):
cube = Cube(**cubeinputs)
webspec, specmsg, badspots = getWebSpectrum(cube, x, y, xyorig='lower')
msg = 'gettin some spaxel with (x={0}, y={1})'.format(x, y)
if not webspec:
self.galaxy['error'] = 'Error: {0}'.format(specmsg)
status = -1
else:
status = 1
output = {'message': msg, 'specmsg': specmsg, 'spectra': webspec, 'status': status, 'badspots': badspots}
else:
output = {'specmsg': 'Error: X or Y not specified for map', 'status': -1}
self.galaxy['error'] = output['specmsg']
else:
output = {'specmsg': 'Error: No maptype specified in request', 'status': -1}
self.galaxy['error'] = output['specmsg']
return jsonify(result=output)
def webtable(self):
''' Do a query for Bootstrap Table interaction in Marvin web '''
form = processRequest(request=request)
args = av.manual_parse(self, request, use_params='query')
# remove args
__tmp__ = args.pop('release', None)
__tmp__ = args.pop('searchfilter', None)
limit = args.get('limit')
offset = args.get('offset')
if 'sort' in args:
current_session['query_sort'] = args['sort']
# set parameters
searchvalue = current_session.get('searchvalue', None)
returnparams = current_session.get('returnparams', None)
# exit if no searchvalue is found
if not searchvalue:
output = jsonify({'errmsg': 'No searchvalue found', 'status': -1})
return output
# this is to fix the brokeness with sorting on a table column using remote names
print('rp', returnparams, args)
# do query
try:
q, res = doQuery(searchfilter=searchvalue,
release=self._release,
returnparams=returnparams,
**args)
except Exception as e:
errmsg = 'Error generating webtable: {0}'.format(e)
output = jsonify({'status': -1, 'errmsg': errmsg})
return output
# get subset on a given page
try:
__results__ = res.getSubset(offset, limit=limit)
except Exception as e:
errmsg = 'Error getting table page: {0}'.format(e)
output = jsonify({'status': -1, 'errmsg': errmsg})
return output
else:
# get keys
cols = res.columns.remote
# create output
rows = res.getDictOf(format_type='listdict')
output = {
'total': res.totalcount,
'rows': rows,
'columns': cols,
'limit': limit,
'offset': offset
}
output = jsonify(output)
return output
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')
# datamodel
dm = datamodel[self._dapver]
# 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 = [p.full(web=True) for p in dm.properties]
dapdefaults = dm.get_default_mapset()
# 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
output['image'] = get_manga_image(cube)
output['spectra'] = webspec
output['specmsg'] = specmsg
output['maps'] = mapdict
output['mapmsg'] = mapmsg
output['dapmaps'] = daplist
output['dapmapselect'] = dapdefaults
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 index(self):
'''Returns general cube info
.. :quickref: Cube; Get general cube info
:query string release: the release of MaNGA
:resjson int status: status of response. 1 if good, -1 if bad.
:resjson string error: error message, null if None
:resjson json inconfig: json of incoming configuration
:resjson json utahconfig: json of outcoming configuration
:resjson string traceback: traceback of an error, null if None
:resjson string data: data message
:resheader Content-Type: application/json
:statuscode 200: no error
:statuscode 422: invalid input parameters
**Example request**:
.. sourcecode:: http
GET /marvin/api/cubes/ HTTP/1.1
Host: api.sdss.org
Accept: application/json, */*
**Example response**:
.. sourcecode:: http
HTTP/1.1 200 OK
Content-Type: application/json
{
"status": 1,
"error": null,
"inconfig": {"release": "MPL-5"},
"utahconfig": {"release": "MPL-5", "mode": "local"},
"traceback": null,
"data": "this is a cube!"
}
'''
av.manual_parse(self, request)
self.results['status'] = 1
self.results['data'] = 'this is a cube!'
return jsonify(self.results)
def selectmpl(self):
''' Global selection of the MPL/DR versions '''
args = av.manual_parse(self, request, use_params='index')
version = args.get('release', None)
current_session['release'] = version
drpver, dapver = config.lookUpVersions(release=version)
current_session['drpver'] = drpver
current_session['dapver'] = dapver
out = {'status': 1, 'msg': 'Success', 'current_release': version,
'current_drpver': drpver, 'current_dapver': dapver}
return jsonify(result=out)
def get(self, plateid):
''' Retrieve info for a given plate id '''
# validate the input
args = av.manual_parse(self, request)
self.plate['plateid'] = args.get('plateid')
pinputs = {
'plate': plateid,
'mode': 'local',
'nocubes': True,
'release': self._release
}
try:
plate = mPlate(**pinputs)
except MarvinError as e:
self.plate['plate'] = None
self.plate['drpver'] = self._drpver
self.plate[
'error'] = 'Could not grab Plate for id {0}: {1}'.format(
plateid, e)
else:
self.plate['plate'] = plate
self.plate['drpver'] = plate._drpver
tmpfile = plate._getFullPath(url=True)
self.plate['sasurl'] = plate.platedir
# Get images for plate
imfiles = None
try:
imfiles = getImagesByPlate(plateid=plateid,
as_url=True,
mode='local',
release=self._release)
except MarvinError as e:
self.plate[
'error'] = 'Error: could not get images for plate {0}: {1}'.format(
plateid, e)
else:
# thumbs = [imfiles.pop(imfiles.index(t)) if 'thumb' in t else t for t in imfiles]
# plateifu = ['-'.join(re.findall('\d{3,5}', im)) for im in imfiles]
images = buildImageDict(imfiles)
# if image grab failed, make placeholders
if not imfiles:
images = buildImageDict(imfiles, test=True, num=29)
# Add images to dict
self.plate['images'] = images
return render_template('plate.html', **self.plate)
def webtable(self):
''' Do a query for Bootstrap Table interaction in Marvin web '''
form = processRequest(request=request)
args = av.manual_parse(self, request, use_params='query')
#{'sort': u'cube.mangaid', 'task': None, 'end': None, 'searchfilter': None,
#'paramdisplay': None, 'start': None, 'rettype': None, 'limit': 10, 'offset': 30,
#'release': u'MPL-4', 'params': None, 'order': u'asc'}
# remove args
__tmp__ = args.pop('release', None)
__tmp__ = args.pop('searchfilter', None)
limit = args.get('limit')
offset = args.get('offset')
# set parameters
searchvalue = current_session.get('searchvalue', None)
returnparams = current_session.get('returnparams', None)
# limit = form.get('limit', 10, type=int)
# offset = form.get('offset', None, type=int)
# order = form.get('order', None, type=str)
# sort = form.get('sort', None, type=str)
# search = form.get('search', None, type=str)
# exit if no searchvalue is found
if not searchvalue:
output = jsonify({
'webtable_error': 'No searchvalue found',
'status': -1
})
return output
# do query
q, res = doQuery(searchfilter=searchvalue,
release=self._release,
returnparams=returnparams,
**args)
# q, res = doQuery(searchfilter=searchvalue, release=self._release,
# limit=limit, order=order, sort=sort, returnparams=returnparams)
# get subset on a given page
__results__ = res.getSubset(offset, limit=limit)
# get keys
cols = res.mapColumnsToParams()
# create output
rows = res.getDictOf(format_type='listdict')
output = {'total': res.totalcount, 'rows': rows, 'columns': cols}
output = jsonify(output)
return output
def galidselect(self):
''' Route that handle the Navbar plate/galaxy id search form '''
args = av.manual_parse(self, request, use_params='index', required='galid')
galid = args.get('galid', None)
if not galid:
# if not galid return main page
return redirect(url_for('index_page.Marvin:index'))
else:
idtype = parseIdentifier(galid)
# check the idtype
if idtype == 'plateifu' or idtype == 'mangaid':
return redirect(url_for('galaxy_page.Galaxy:get', galid=galid))
elif idtype == 'plate':
return redirect(url_for('plate_page.Plate:get', plateid=galid))
else:
return redirect(url_for('index_page.Marvin:index'))
def init_nsaplot(self):
args = av.manual_parse(self, request, use_params='galaxy', required='plateifu')
#self._drpver, self._dapver, self._release = parseSession()
cubeinputs = {'plateifu': args.get('plateifu'), 'release': self._release}
# get the default nsa choices
nsachoices = self.galaxy.get('nsachoices', None)
if not nsachoices:
nsachoices = {'1': {'y': 'z', 'x': 'elpetro_logmass', 'xtitle': 'Stellar Mass',
'ytitle': 'Redshift', 'title': 'Redshift vs Stellar Mass'},
'2': {'y': 'elpetro_absmag_g_r', 'x': 'elpetro_absmag_i', 'xtitle': 'AbsMag_i',
'ytitle': 'Abs. g-r', 'title': 'Abs. g-r vs Abs. Mag i'}}
# get cube (self.galaxy['cube'] does not work)
try:
cube = Cube(**cubeinputs)
except Exception as e:
cube = None
# get some nsa params
if not cube:
output = {'nsamsg': 'No cube found', 'nsa': None, 'status': -1}
else:
# get the galaxy nsa parameters
cols = self.galaxy.get('nsaplotcols')
try:
nsadict, nsacols = make_nsa_dict(cube.nsa)
nsa = {args.get('plateifu'): nsadict}
except Exception as e:
output = {'nsamsg': e.message, 'status': -1, 'nsa': None}
else:
# get the sample nsa parameters
try:
nsacache = 'nsa_{0}'.format(self._release.lower().replace('-', ''))
nsadict = get_nsa_dict(nsacache, self._drpver)
except Exception as e:
output = {'nsamsg': 'Failed to retrieve sample NSA: {0}'.format(e), 'status': -1, 'nsa': nsa, 'nsachoices': nsachoices}
else:
#nsadict = [(_db_row_to_dict(n[0], remove_columns=['pk', 'catalogue_pk']), n[1]) for n in allnsa]
nsasamp = {c: [n[0][c.split('_i')[0]][5] if 'absmag_i' in c or 'mtol_i' in c else n[0][c] for n in nsadict] for c in cols}
nsasamp['plateifu'] = [n[1] for n in nsadict]
nsasamp = remove_nans(nsasamp)
nsa['sample'] = nsasamp
output = {'nsamsg': None, 'status': 1, 'nsa': nsa, 'nsachoices': nsachoices, 'nsaplotcols': cols}
return jsonify(result=output)
def get_spaxel_cache(*args, **kwargs):
''' Function used to generate the route cache key
Cache key when using cache.memoize or cache.cached decorator.
memoize remembers input methods arguments; cached does not.
Parameters:
args (list):
a list of the fx/method route call and object instance (self)
kwargs (dict):
a dictonary of arguments passed into the method
Returns:
A string used for the cache key lookup
'''
# get the method and self instance
fxn, inst = args
# parse the form request to extract any parameters
reqargs = av.manual_parse(inst, request, use_params='galaxy', required=['plateifu', 'type'], makemulti=True)
maptype = reqargs.get('type', None)
if maptype == 'optical':
mousecoords = reqargs.getlist('mousecoords[]', type=float)
infile = current_session['imagefile']
radec = convertImgCoords(mousecoords, infile, to_radec=True)
ww = WCS(current_session['wcs'])
cube_shape = [current_session['cube_shape']] * 2
y, x = convertCoords(radec, wcs=ww, shape=cube_shape,
mode='sky', xyorig='lower').T
y = y[0]
x = x[0]
elif maptype == 'heatmap':
x = reqargs.get('x', None, type=int)
y = reqargs.get('y', None, type=int)
plateifu = reqargs.get('plateifu').replace('-', '_')
release = inst._release.lower().replace('-', '')
# create unique cache key name
key = 'getspaxel_{0}_{1}_{2}_{3}'.format(
release, plateifu, x, y)
return key
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 index(self):
# Attempt to retrieve search parameters
form = processRequest(request=request)
self.search['formparams'] = form
self.search['latest_dr'] = self._release.lower() if 'DR' in self._release else config._get_latest_release(dr_only=True).lower()
# set the search form and form validation
searchform = self.mf.SearchForm(form)
searchform.returnparams.choices = [(k.lower(), k) for k in query_params.list_params()]
# Add the forms and parameters
self.search['paramdata'] = query_params
self.search['guideparams'] = [{'id': p.full, 'optgroup': group.name, 'type': 'double' if p.dtype == 'float' else p.dtype, 'validation': {'step': 'any'}} for group in query_params for p in group]
self.search['searchform'] = searchform
self.search['placeholder'] = getRandomQuery()
self.search['returnurl'] = 'https://sdss-marvin.readthedocs.io/en/stable/datamodel/{0}.html#{0}query'.format(
current_session['release'].lower().replace('-', ''))
# If form parameters then try to do a search
if form:
self.search.update({'results': None, 'errmsg': None})
args = av.manual_parse(self, request, use_params='search')
# get form parameters
searchvalue = form['searchbox'] # search filter input
returnparams = form.getlist('returnparams', type=str) # dropdown select
self.search.update({'returnparams': returnparams})
current_session.update({'searchvalue': searchvalue, 'returnparams': returnparams})
# if main form passes validation then do search
if searchform.validate():
# try the query
try:
q, res = doQuery(search_filter=searchvalue, release=self._release, return_params=returnparams)
except (MarvinError, KeyError) as e:
self.search['errmsg'] = 'Could not perform query: {0}'.format(refine_error(e))
except NotImplementedError as e: # DAP queries disabled
self.search['errmsg'] = 'Could not perform query: {0}'.format(e)
else:
self.search['filter'] = q.search_filter
self.search['count'] = res.totalcount
self.search['runtime'] = res.query_time.total_seconds()
if res.count > 0:
cols = res.columns.remote
rows = res.getDictOf(format_type='listdict')
output = {'total': res.totalcount, 'rows': rows, 'columns': cols, 'limit': None, 'offset': None}
else:
output = None
self.search['results'] = output
self.search['reslen'] = len(res.results)
if returnparams:
returnparams = [str(r) for r in returnparams]
rpstr = 'return_params={0} <br>'.format(returnparams) if returnparams else ''
qstr = ', return_params=returnparams' if returnparams else ''
self.search['querystring'] = ("<html><samp>from marvin.tools.query import Query<br>\
myfilter='{0}'<br> {1}\
q = Query(search_filter=myfilter{2})<br>\
r = q.run()<br></samp></html>".format(searchvalue, rpstr, qstr))
return render_template('search.html', **self.search)
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 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')
# datamodel
dm = datamodel[self._dapver]
# turning toggle on
nowebsession = marvin.config._custom_config.get('no_web_session', None)
if not nowebsession:
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, badspots = getWebSpectrum(cube,
cube.ra,
cube.dec,
byradec=True)
daplist = [p.full(web=True) for p in dm.properties]
dapdefaults = dm.get_default_mapset()
# select any DAP maps and bin-template from the session
selected_bintemp = current_session.get('bintemp', None)
selected_maps = current_session.get('selected_dapmaps', dapdefaults)
# check for correct bintemp
if selected_bintemp and selected_bintemp not in dm.get_bintemps(
db_only=True):
selected_bintemp = '{0}-{1}'.format(dm.get_bintype(),
dm.get_template())
# build the uber map dictionary
try:
mapdict = buildMapDict(cube,
selected_maps,
self._dapver,
bintemp=selected_bintemp)
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
output['image'] = cube.getImage().url
output['spectra'] = webspec
output['specmsg'] = specmsg
output['maps'] = mapdict
output['mapmsg'] = mapmsg
output['dapmaps'] = daplist
output['dapmapselect'] = selected_maps
output['daplines'] = dm.get_channels('emline_gflux', formatted=True)
output['badspots'] = badspots
output['dapbintemps'] = dm.get_bintemps(db_only=True)
if 'bintemp' not in current_session:
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 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)
def index(self):
# Attempt to retrieve search parameters
form = processRequest(request=request)
self.search['formparams'] = form
print('search form', form, type(form))
# set the search form and form validation
searchform = self.mf.SearchForm(form)
q = Query(release=self._release)
# allparams = q.get_available_params()
bestparams = q.get_best_params()
searchform.returnparams.choices = [(k.lower(), k) for k in bestparams]
searchform.parambox.validators = [
all_in(bestparams), validators.Optional()
]
# Add the forms
self.search['searchform'] = searchform
self.search['placeholder'] = getRandomQuery()
#from flask import abort
#abort(500)
# If form parameters then try to do a search
if form:
self.search.update({'results': None, 'errmsg': None})
args = av.manual_parse(self, request, use_params='search')
print('search args', args)
# get form parameters
searchvalue = form['searchbox'] # search filter input
returnparams = form.getlist('returnparams',
type=str) # dropdown select
parambox = form.get('parambox', None,
type=str) # from autocomplete
if parambox:
parms = parambox.split(',')
parms = parms if parms[-1].strip() else parms[:-1]
parambox = parms if parambox else None
# Select the one that is not none
returnparams = returnparams if returnparams and not parambox else \
parambox if parambox and not returnparams else \
list(set(returnparams) | set(parambox)) if returnparams and parambox else None
print('return params', returnparams)
current_session.update({
'searchvalue': searchvalue,
'returnparams': returnparams
})
# if main form passes validation then do search
if searchform.validate():
# try the query
try:
q, res = doQuery(searchfilter=searchvalue,
release=self._release,
returnparams=returnparams)
except MarvinError as e:
self.search[
'errmsg'] = 'Could not perform query: {0}'.format(e)
else:
self.search['filter'] = q.strfilter
self.search['count'] = res.totalcount
self.search['runtime'] = res.query_runtime.total_seconds()
if res.count > 0:
cols = res.mapColumnsToParams()
rows = res.getDictOf(format_type='listdict')
output = {
'total': res.totalcount,
'rows': rows,
'columns': cols
}
else:
output = None
self.search['results'] = output
self.search['reslen'] = len(res.results)
if returnparams:
returnparams = [str(r) for r in returnparams]
rpstr = 'returnparams={0} <br>'.format(
returnparams) if returnparams else ''
qstr = ', returnparams=returnparams' if returnparams else ''
self.search['querystring'] = (
"<html><samp>from marvin import \
config<br>from marvin.tools.query import Query<br>config.mode='remote'<br>\
filter='{0}'<br> {1}\
q = Query(searchfilter=filter{2})<br>\
r = q.run()<br></samp></html>".format(
searchvalue, rpstr, qstr))
return render_template('search.html', **self.search)