def getDir3d(inputid, mode=None, release=None):
''' Get the 3d redux Image directory from an input plate or plate-IFU '''
idtype = parseIdentifier(inputid)
if idtype == 'plate':
plateid = inputid
elif idtype == 'plateifu':
plateid, __ = inputid.split('-')
release = marvin.config.release if not release else release
drpver, __ = marvin.config.lookUpVersions(release=release)
if check_versions(drpver, 'v1_5_4'):
from marvin.tools.plate import Plate
try:
plate = Plate(plate=plateid, nocubes=True, mode=mode, release=release)
except Exception as e:
raise MarvinError('Could not retrieve a remote plate. If it is a mastar '
'plate you are after, Marvin currently does not handle those: {0}'.format(e))
else:
dir3d = plate.dir3d
else:
dir3d = 'stack'
return dir3d
def _getRSS(name, **kwargs):
"""Retrieves a RSS Marvin object."""
rss = None
results = {}
# Pop the release to remove a duplicate input to Maps
release = kwargs.pop('release', None)
# parse name into either mangaid or plateifu
try:
idtype = parseIdentifier(name)
except Exception as e:
results['error'] = 'Failed to parse input name {0}: {1}'.format(name, str(e))
return rss, results
try:
if idtype == 'plateifu':
plateifu = name
mangaid = None
elif idtype == 'mangaid':
mangaid = name
plateifu = None
else:
raise MarvinError('invalid plateifu or mangaid: {0}'.format(idtype))
rss = RSS(mangaid=mangaid, plateifu=plateifu, mode='local', release=release)
results['status'] = 1
except Exception as e:
results['error'] = 'Failed to retrieve RSS {0}: {1}'.format(name, str(e))
return rss, results
def __init__(self, targetid, vacfile, **kwargs):
self.targetid = targetid
self._ttype = parseIdentifier(targetid)
assert self._ttype in ['plateifu', 'mangaid'], 'Input targetid must be a valid plateifu or mangaid'
self._vacfile = vacfile
self._data = self._get_data(self._vacfile)
self._indata = targetid in self._data[self._ttype]
def _getRSS(name, use_file=True, release=None, **kwargs):
"""Retrieves a RSS Marvin object."""
drpver, __ = marvin.config.lookUpVersions(release)
rss = None
results = {}
# parse name into either mangaid or plateifu
try:
idtype = parseIdentifier(name)
except Exception as ee:
results['error'] = 'Failed to parse input name {0}: {1}'.format(name, str(ee))
return rss, results
filename = None
plateifu = None
mangaid = None
try:
if use_file:
if idtype == 'mangaid':
plate, ifu = mangaid2plateifu(name, drpver=drpver)
elif idtype == 'plateifu':
plate, ifu = name.split('-')
if Path is not None:
filename = Path().full('mangarss', ifu=ifu, plate=plate, drpver=drpver)
assert os.path.exists(filename), 'file not found.'
else:
raise MarvinError('cannot create path for MaNGA rss.')
else:
if idtype == 'plateifu':
plateifu = name
elif idtype == 'mangaid':
mangaid = name
else:
raise MarvinError('invalid plateifu or mangaid: {0}'.format(idtype))
rss = marvin.tools.RSS(filename=filename, mangaid=mangaid, plateifu=plateifu,
mode='local', release=release)
results['status'] = 1
except Exception as ee:
results['error'] = 'Failed to retrieve RSS {0}: {1}'.format(name, str(ee))
return rss, results
def _getCube(name, use_file=False, release=None, **kwargs):
''' Retrieve a cube using marvin tools '''
drpver, __ = config.lookUpVersions(release)
cube = None
results = {}
# parse name into either mangaid or plateifu
try:
idtype = parseIdentifier(name)
except Exception as ee:
results['error'] = 'Failed to parse input name {0}: {1}'.format(name, str(ee))
return cube, results
filename = None
plateifu = None
mangaid = None
try:
if use_file:
if idtype == 'mangaid':
plate, ifu = mangaid2plateifu(name, drpver=drpver)
elif idtype == 'plateifu':
plate, ifu = name.split('-')
if Path is not None:
filename = Path(release=release).full('mangacube', ifu=ifu, plate=plate, drpver=drpver, wave='LOG')
assert os.path.exists(filename), 'file not found.'
else:
raise MarvinError('cannot create path for MaNGA cube.')
else:
if idtype == 'plateifu':
plateifu = name
elif idtype == 'mangaid':
mangaid = name
else:
raise MarvinError('invalid plateifu or mangaid: {0}'.format(idtype))
cube = Cube(filename=filename, mangaid=mangaid, plateifu=plateifu,
mode='local', release=release)
results['status'] = 1
except Exception as ee:
results['error'] = 'Failed to retrieve cube {0}: {1}'.format(name, str(ee))
return cube, results
def has_target(self, target):
''' Checks if a target is contained within the VAC
Parameters:
target (str):
The name of the target
Returns:
A boolean indicating if the target is in the VAC or not
'''
assert isinstance(target, six.string_types), 'target must be a string'
targ_type = parseIdentifier(target)
ttypes = ['plateifu', 'mangaid']
other = ttypes[ttypes.index(targ_type) - 1]
data = self.data[1].data
assert targ_type in map(str.lower, data.columns.names), \
'Identifier "{0}" is not available. Try a "{1}".'.format(targ_type, other)
return target in data[targ_type]
def _getSpaxel(name, x, y, **kwargs):
"""Retrieves a Marvin Spaxel object."""
spaxel = None
results = {}
# Pop the release to remove a duplicate input to Maps
release = kwargs.pop('release', None)
# parse name into either mangaid or plateifu
try:
idtype = parseIdentifier(name)
except Exception as e:
results['error'] = 'Failed to parse input name {0}: {1}'.format(
name, str(e))
return spaxel, results
try:
if idtype == 'plateifu':
plateifu = name
mangaid = None
elif idtype == 'mangaid':
mangaid = name
plateifu = None
else:
raise MarvinError(
'invalid plateifu or mangaid: {0}'.format(idtype))
spaxel = Spaxel(x=x,
y=y,
mangaid=mangaid,
plateifu=plateifu,
release=release,
**kwargs)
results['status'] = 1
except Exception as e:
results['error'] = 'Failed to retrieve Spaxels {0}: {1}'.format(
name, str(e))
return spaxel, results
def _getCube(name, **kwargs):
''' Retrieve a cube using marvin tools '''
# Pop the release to remove a duplicate input to Maps
release = kwargs.pop('release', None)
cube = None
results = {}
# parse name into either mangaid or plateifu
try:
idtype = parseIdentifier(name)
except Exception as ee:
results['error'] = 'Failed to parse input name {0}: {1}'.format(
name, str(ee))
return cube, results
try:
if idtype == 'plateifu':
plateifu = name
mangaid = None
elif idtype == 'mangaid':
mangaid = name
plateifu = None
else:
raise MarvinError(
'invalid plateifu or mangaid: {0}'.format(idtype))
cube = Cube(mangaid=mangaid,
plateifu=plateifu,
mode='local',
release=release)
results['status'] = 1
except Exception as ee:
results['error'] = 'Failed to retrieve cube {0}: {1}'.format(
name, str(ee))
return cube, results
def _get_model_cube(name, **kwargs):
"""Retrieves a Marvin ModelCube object."""
model_cube = None
results = {}
# Pop the release to remove a duplicate input to Maps
release = kwargs.pop('release', None)
# parse name into either mangaid or plateifu
try:
idtype = parseIdentifier(name)
except Exception as err:
results['error'] = 'Failed to parse input name {0}: {1}'.format(
name, str(err))
return model_cube, results
try:
if idtype == 'plateifu':
plateifu = name
mangaid = None
elif idtype == 'mangaid':
mangaid = name
plateifu = None
else:
raise MarvinError(
'invalid plateifu or mangaid: {0}'.format(idtype))
model_cube = ModelCube(mangaid=mangaid,
plateifu=plateifu,
release=release,
**kwargs)
results['status'] = 1
except Exception as err:
results['error'] = 'Failed to retrieve ModelCube {0}: {1}'.format(
name, str(err))
return model_cube, results
def _get_model_cube(name, use_file=False, release=None, **kwargs):
"""Retrieves a Marvin ModelCube object."""
model_cube = None
results = {}
drpver, dapver = config.lookUpVersions(release)
# parse name into either mangaid or plateifu
try:
idtype = parseIdentifier(name)
except Exception as err:
results['error'] = 'Failed to parse input name {0}: {1}'.format(
name, str(err))
return model_cube, results
filename = None
plateifu = None
mangaid = None
bintype = kwargs.pop('bintype')
template = kwargs.pop('template')
try:
if use_file:
if idtype == 'mangaid':
plate, ifu = mangaid2plateifu(name, drpver=drpver)
elif idtype == 'plateifu':
plate, ifu = name.split('-')
if Path is not None:
daptype = '{0}-{1}'.format(bintype, template)
filename = Path().full('mangadap5',
ifu=ifu,
drpver=drpver,
dapver=dapver,
plate=plate,
mode='LOGCUBE',
daptype=daptype)
assert os.path.exists(filename), 'file not found.'
else:
raise MarvinError('cannot create path for MaNGA cube.')
else:
if idtype == 'plateifu':
plateifu = name
elif idtype == 'mangaid':
mangaid = name
else:
raise MarvinError(
'invalid plateifu or mangaid: {0}'.format(idtype))
model_cube = ModelCube(filename=filename,
mangaid=mangaid,
plateifu=plateifu,
release=release,
template=template,
bintype=bintype,
**kwargs)
results['status'] = 1
except Exception as err:
results['error'] = 'Failed to retrieve ModelCube {0}: {1}'.format(
name, str(err))
return model_cube, results
def getImagesByList(inputlist, download=False, mode=None, as_url=None, verbose=None, release=None):
''' Get all images from a list of ids
.. deprecated:: 2.3.0
Use :class:`marvin.utils.general.images.get_images_by_list` instead.
Retrieve a list of images from either your local filesystem SAS
or the Utah SAS. Optionally can download the images by rsync using
sdss_access.
When as_url is False, both local and remote modes will allow you to access
the full path to the images in your local SAS. WHen as_url is True,
local mode generates the Utah SAS url links, while remote mode generates the
Utah SAS rsync links.
Auto mode defaults to remote.
Parameters:
inputlist (list):
A list of plate-ifus or mangaids for the images you want to retrieve. Required.
download (bool):
Set to download the images from the SAS. Only works in remote mode.
mode ({'local', 'remote', 'auto'}):
The load mode to use. See
:doc:`Mode secision tree</mode_decision>`.
the cube exists.
as_url (bool):
Convert the list of images to use the SAS url (mode=local)
or the SAS rsync url (mode=remote)
verbose (bool):
Turns on verbosity during rsync
release (str):
The release version of the images to return
Returns:
listofimages (list):
The list of images you have requested
'''
warnings.warn('getImagesByList is deprecated as of Marvin 2.3.0. '
'Please use get_images_by_list', MarvinDeprecationWarning)
# Check inputs
assert isinstance(inputlist, (list, np.ndarray)), 'Input must be of type list or Numpy array'
idtype = parseIdentifier(inputlist[0])
assert idtype in ['plateifu', 'mangaid'], 'Input must be of type plate-ifu or mangaid'
# mode is checked via decorator
# convert mangaids into plateifus
if idtype == 'mangaid':
newlist = []
for myid in inputlist:
try:
plateifu = mangaid2plateifu(myid)
except MarvinError:
plateifu = None
newlist.append(plateifu)
inputlist = newlist
# setup Rsync Access
release = release if release else marvin.config.release
drpver, __ = marvin.config.lookUpVersions(release=release)
is_public = 'DR' in release
rsync_release = release.lower() if is_public else None
rsync_access = RsyncAccess(label='marvin_getlist', verbose=verbose, public=is_public,
release=rsync_release)
imgname = 'mangaimagenew' if check_versions(drpver, 'v2_5_3') else 'mangaimage'
# if mode is auto, set it to remote:
if mode == 'auto':
warnings.warn('Mode is auto. Defaulting to remote. If you want to access your '
'local images, set the mode explicitly to local', MarvinUserWarning)
mode = 'remote'
# do a local or remote thing
if mode == 'local':
# Get list of images
listofimages = []
for plateifu in inputlist:
dir3d = getDir3d(plateifu, mode=mode, release=release)
plateid, ifu = plateifu.split('-')
if as_url:
path = rsync_access.url(imgname, plate=plateid, drpver=drpver, ifu=ifu, dir3d=dir3d)
else:
path = rsync_access.full(imgname, plate=plateid, drpver=drpver, ifu=ifu, dir3d=dir3d)
listofimages.append(path)
# if download, issue warning that cannot do it
if download:
warnings.warn('Download not available when in local mode', MarvinUserWarning)
return listofimages
elif mode == 'remote':
rsync_access.remote()
# Add plateifus to stream
for plateifu in inputlist:
dir3d = getDir3d(plateifu, mode=mode, release=release)
plateid, ifu = plateifu.split('-')
rsync_access.add(imgname, plate=plateid, drpver=drpver, ifu=ifu, dir3d=dir3d)
# set the stream
try:
rsync_access.set_stream()
except AccessError as e:
raise MarvinError('Error with sdss_access rsync.set_stream. AccessError: {0}'.format(e))
# get the list
listofimages = rsync_access.get_urls() if as_url else rsync_access.get_paths()
if download:
rsync_access.commit()
else:
return listofimages
