def _checkFilename(self):
''' Checks the filename for a proper FITS file '''
# if filename is not FITS, then try to load one
if 'fits' not in self.filename.lower():
if not Path:
raise MarvinError('sdss_access is not installed')
else:
# is_public = 'DR' in self._release
# path_release = self._release.lower() if is_public else None
sdss_path = Path(release=self._release)
# try a cube
full = sdss_path.full('mangacube', drpver=self._drpver, plate=self.plateid, ifu='*', wave='LOG')
cubeexists = sdss_path.any('', full=full)
if cubeexists:
file = sdss_path.one('', full=full)
else:
# try an rss
full = sdss_path.full('mangarss', drpver=self._drpver, plate=self.plateid, ifu='*', wave='LOG')
rssexists = sdss_path.any('', full=full)
if rssexists:
file = sdss_path.one('', full=full)
else:
file = None
# load the file
if file:
self.filename = file
else:
self.filename = None
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 __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)
class Galaxy(object):
"""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):
"""Initialize plate and ifu."""
self.plateifu = plateifu
self.plate, self.ifu = self.plateifu.split('-')
self.plate = int(self.plate)
def set_galaxy_data(self, data_origin=None):
"""Set galaxy properties from the configuration file."""
if self.plateifu not in galaxy_data:
return
data = copy.deepcopy(galaxy_data[self.plateifu])
for key in data.keys():
setattr(self, key, data[key])
# sets specfic data per release
releasedata = self.releasedata[self.release]
for key in releasedata.keys():
setattr(self, key, releasedata[key])
# remap NSA drpall names for MPL-4 vs 5+
drpcopy = self.nsa_data['drpall'].copy()
for key, val in self.nsa_data['drpall'].items():
if isinstance(val, list):
newval, newkey = drpcopy.pop(key)
if self.release == 'MPL-4':
drpcopy[newkey] = newval
else:
drpcopy[key] = newval
self.nsa_data['drpall'] = drpcopy
def set_params(self, bintype=None, template=None, release=None):
"""Set bintype, template, etc."""
self.release = release
self.drpver, self.dapver = config.lookUpVersions(self.release)
self.drpall = 'drpall-{0}.fits'.format(self.drpver)
self.bintype = datamodel[self.dapver].get_bintype(bintype)
self.template = datamodel[self.dapver].get_template(template)
self.bintemp = '{0}-{1}'.format(self.bintype.name, self.template.name)
if release == 'MPL-4':
self.niter = int('{0}{1}'.format(self.template.n, self.bintype.n))
else:
self.niter = '*'
self.access_kwargs = {
'plate': self.plate,
'ifu': self.ifu,
'drpver': self.drpver,
'dapver': self.dapver,
'dir3d': self.dir3d,
'mpl': self.release,
'bintype': self.bintype.name,
'n': self.niter,
'mode': '*',
'daptype': self.bintemp
}
def set_filepaths(self, pathtype='full'):
"""Set the paths for cube, maps, etc."""
self.path = Path()
self.imgpath = self.path.__getattribute__(pathtype)(
'mangaimage', **self.access_kwargs)
self.cubepath = self.path.__getattribute__(pathtype)(
'mangacube', **self.access_kwargs)
self.rsspath = self.path.__getattribute__(pathtype)(
'mangarss', **self.access_kwargs)
if self.release == 'MPL-4':
self.mapspath = self.path.__getattribute__(pathtype)(
'mangamap', **self.access_kwargs)
self.modelpath = None
else:
self.access_kwargs.pop('mode')
self.mapspath = self.path.__getattribute__(pathtype)(
'mangadap5', mode='MAPS', **self.access_kwargs)
self.modelpath = self.path.__getattribute__(pathtype)(
'mangadap5', mode='LOGCUBE', **self.access_kwargs)
def get_location(self, path):
"""Extract the location from the input path."""
return self.path.location("", full=path)
def partition_path(self, path):
"""Partition the path into non-redux/analysis parts."""
endredux = path.partition(self.mangaredux)[-1]
endanalysis = path.partition(self.mangaanalysis)[-1]
end = (endredux or endanalysis)
return end
def new_path(self, name, newvar):
''' Sets a new path with the subsituted name '''
access_copy = self.access_kwargs.copy()
access_copy['mode'] = '*'
access_copy.update(**newvar)
if name == 'maps':
access_copy['mode'] = 'MAPS'
name = 'mangamap' if self.release == 'MPL-4' else 'mangadap5'
elif name == 'modelcube':
access_copy['mode'] = 'LOGCUBE'
name = None if self.release == 'MPL-4' else 'mangadap5'
path = self.path.full(name, **access_copy) if name else None
return path