def getInterpModels(interpolatedDimensions, SQL, boundaryValues, deckShape):
conn = modeldb.getModelDBConn()
dimensions = ', '.join(interpolatedDimensions)
if len(dimensions) > 0:
positions = conn.execute('select %s %s' % (
dimensions,
SQL,
), boundaryValues).fetchall()
# There is a bug that if the length of each position is one, then instead
# of returning a tuple it should return a float
for i, position in enumerate(positions):
if len(position) == 1:
positions[i] = position[0]
else:
positions = []
modelGrid = conn.execute('select deck %s' % (SQL, ),
boundaryValues).fetchall()
conn.close()
print
return positions, np.array(
[item.reshape(deckShape) for item in zip(*modelGrid)[0]])
def getInterpModels(interpolatedDimensions, SQL, boundaryValues, deckShape):
conn = modeldb.getModelDBConn()
dimensions = ', '.join(interpolatedDimensions)
if len(dimensions) > 0:
positions = conn.execute('select %s %s' % (dimensions, SQL,),
boundaryValues).fetchall()
# There is a bug that if the length of each position is one, then instead
# of returning a tuple it should return a float
for i, position in enumerate(positions):
if len(position) == 1:
positions[i] = position[0]
else: positions = []
modelGrid = conn.execute('select deck %s' % (SQL,),
boundaryValues).fetchall()
conn.close()
print
return positions, np.array([item.reshape(deckShape) for item in zip(*modelGrid)[0]])
def installedModels():
"""
Reads from the database and returns the models on disk
"""
conn = modeldb.getModelDBConn()
modelData = conn.execute("SELECT model_name FROM atmosphy_conf WHERE installed=1")
modelNames = ([str(item[0]) for item in modelData])
#modelNames.remove('models')
return modelNames
def importModel(modelName, modelID):
"importing model into the database"
atmosphy_path = os.path.expanduser('~/.atmosphy')
conn = modeldb.getModelDBConn()
deckShape = conn.execute('select ROWS, COLS from ATMOSPHY_CONF '
'where MODEL_NAME=?', (modelName,)).fetchone()
for fname in glob(os.path.join(atmosphy_path, 'models', modelName, '*.dat')):
modelSrc = file(fname).read()
modelsRawData = re.split('B?EGIN\s+ITERATION\s+\d+\s+COMPLETED',modelSrc)
for model in modelsRawData:
#problem with split
if model == '\n' or model == '': continue
teffLoggMatch = re.search('T?EFF\s+(\d+\.\d*)\s+GRAVITY\s+(\d+\.\d*)',model)
#searching for metallicity, alpha and microturbulence
metalAlphaMatch = re.search('\[([\s+-]?\d+\.\d+)([aAbB]?)\]?', model)
microMatch = re.search('VTURB[ =]?(\d+[\.\d+]?)',model)
mixLengthMatch = re.search('ONVECTION (OFF|ON)\s+(\d+\.\d+)',model)
pradkMatch = re.search('P?RADK (\d+\.\d+E[+-]?\d+)',model)
#Checking the integrity of the model
if teffLoggMatch == None:
raise casKurImportException(
"Current Model does not contain effective temperature:"
"\n\n--------\n\n%s" % (model,))
try:
if metalAlphaMatch == None:
raise casKurImportException(
"Current Model does not contain metallicity information:"
"\n\n--------\n\n%s" % (model,))
except casKurImportException:
knownProblemFiles = ['ap00k2.dat','ap00k4.dat','asun.dat']
if os.path.basename(fname) in knownProblemFiles:
continue
else:
raise casKurImportException(
"Current Model does not contain metallicity information:"
"\n\n--------\n\n%s" % (model,))
if mixLengthMatch == None:
raise casKurImportException(
"Current Model does not contain mixing length information:"
"\n\n--------\n\n%s" % (model,))
#reading in the model parameters
convertAlpha = {'':0.0, 'a':0.4, 'b':1.0}
teff = float(teffLoggMatch.groups()[0])
logg = float(teffLoggMatch.groups()[1])
feh = float(metalAlphaMatch.groups()[0])
alpha = convertAlpha[metalAlphaMatch.groups()[1].lower()]
micro = float(microMatch.groups()[0])
mixing = float(mixLengthMatch.groups()[1])
pradk = float(pradkMatch.groups()[0])
#reading model, pickling it and compressing it
deck = readDeck(model)
#fix for deck with only 71 points (there seems to be only one in ap05k2odfnew.dat)
if modelName == 'castelli-kurucz' and deck.shape[0] == 71:
continue
if deck.shape != deckShape:
raise ValueError('Deck shape missmatch: expected: %s got %s\n'
'This should not happen please contact the developers of atmosphy' %
(deckShape, deck.shape))
#writing to db
modeldb.insertModelData(conn, modelName, [modelID, teff, logg, feh, alpha, micro, mixing, deck])
logging.info('Added all decks from model %s to db' % modelName)
logging.info('Updating the atmosphy_conf table')
conn.execute('update ATMOSPHY_CONF set rows=?,'
'cols=?, INSTALLED=? where ID=?',
(deck.shape[0], deck.shape[1], 1, modelID))
conn.commit()
conn.close()
def download(modelName, clobber=False, verbose=True, database='~/.atmosphy/atmosphy.db3'):
"""
Download the given model(s) from the Kurucz awebsite and load them into your database.
Parameters:
===========
modelNames : string or list
Downloads all of the model names suppled, or any that match the wildmask supplied.
Available models:
=================
Kurucz : Kuruczs grids of model atmospheres, as described in X
Kurucz-NOVER : Kurucz models with no convective overshooting computed by Fiorella Castelli
[[email protected]] in Trieste. The convective treatment is described in
Castelli, Gratton, and Kuruczs 1997, A&A 328, 841.
Kurucz-ODFNEW : Kurucz models as NOVER but with newly computed ODFs with better opacities
and better abundances.
Kurucz-AODFNEW : Kurucz models as per ODFNEW but with Alpha enhancement. The alpha-process
elements (O, Ne, Mg, Si, S, Ar, Ca, and Ti) enhanced by +0.4 in the log and
Fe -4.53
Examples:
=========
download('Kurucz') : Download the standard Kurucz grid models.
download('Kurucz-*ODFNEW') : This will download both the Kurucz-AODFNEW and the Kurucs-ODFNEW
model as they both match the wildmask given.
"""
atmosphy_path = os.path.expanduser('~/.atmosphy/')
models_path = os.path.join(atmosphy_path, 'models')
conn = modeldb.getModelDBConn()
modelID = conn.execute('select ID from ATMOSPHY_CONF '
'where MODEL_NAME = ?',
(modelName,)).fetchall()
#checking if this model does exist and is not installed
if len(modelID) == 1:
modelID = modelID[0][0]
installed = conn.execute('select INSTALLED from ATMOSPHY_CONF '
'where ID = ?', (modelID,)).fetchone()[0]
if installed == 1:
raise ValueError('Model %s is installed.' % modelName)
elif len(modelID) == 0:
availableModels = conn.execute('select MODEL_NAME from ATMOSPHY_CONF '
'where INSTALLED = 0').fetchall()
print "Available models:\n %s" % ','.join(availableModels)
raise ValueError('Model %s does not exist' % modelName)
# Generate the models directory if it doesn't exist
if not os.path.exists(models_path):
logging.info('Creating %s' % models_path)
os.makedirs(models_path)
# Generate this specific model directory if it doesn't exist
modelDir = os.path.join(models_path, modelName)
if not os.path.exists(os.path.join(models_path, modelName)):
logging.info('Creating %s' % os.path.join(models_path, modelName))
os.makedirs(os.path.join(models_path,modelName))
#Getting models and checking MD5s
curs = conn.cursor()
for url, md5_hash in curs.execute('select URL, MD5_HASH from ATMOSPHY_URLS where MODEL_ID = ?', (modelID,)):
filename = url.split('/')[-1]
if os.path.exists(os.path.join(modelDir, filename)):
print "Checking MD5 for %s" % os.path.join(modelDir, filename),
curMD5 = md5_file(os.path.join(modelDir, filename))
if md5_hash == curMD5:
print "....Verified"
else:
print "....Failed. Redownloading."
stream = urllib2.urlopen(url)
data = stream.read()
stream.close()
newFile = open(os.path.join(modelDir, filename), 'w')
newFile.write(data)
newFile.close()
else:
print "Downloading from %s" % url
stream = urllib2.urlopen(url)
data = stream.read()
stream.close()
newFile = open(os.path.join(modelDir, filename), 'w')
newFile.write(data)
newFile.close()
logging.info('Importing models ...')
importModel(modelName, modelID)
logging.info('Successfully imported %s model' % (modelName,))
logging.info('Done!.')
def interpModelGrid(modelName,
Teff,
logg,
FeH,
k=2.0,
alpha=0.0,
level=1,
method='linear'):
"""
Interpolates in N-dimensional space to find the given point
(Teff, logg, FeH, k, alpha) given the model name.
Parameters:
===========
modelName : string
The name of the model to lookup in your local SQL database.
Teff : float
The effective temperature (Teff in Kelvin) of the star you plan to interpolate for.
FeH : float
The metallicity ([Fe/H]) of the star you plan to interpolate for.
logg : float
The surface gravity (log g) of the star you plan to interpolate for.
k : float, optional (default = 2.0)
The turbulence in the atmosphere of the star (km/s).
alpha : float, optional (default = 0.0)
The level of alpha enhancement of the star ([alpha/Fe] in dex).
level : integer, optional (default = 1)
The maximum number of levels on either side of the point you wish to return in each
dimension.
method : string, optional (default = 'linear')
The interpolation method which is passed to scipy.interpolate.griddata.
Options are 'linear', 'nearest', or 'cubic'.
"""
# Our grid point in N dimensionsal space
gridSpace = {
'teff': Teff,
'logg': logg,
'feh': FeH,
'k': k,
'alpha': alpha
}
conn = modeldb.getModelDBConn()
# Find the nearest neighbours in N dimensions, and get the SQL
interpolatedDimensions, SQL, boundaryValues = getNearestNeighbours(
modelName, Teff, logg, FeH, k, alpha, level=level)
# Populate the model grid
deckShape = conn.execute(
'select ROWS, COLS from ATMOSPHY_CONF where MODEL_NAME=?',
(modelName, )).fetchone()
modelGridCoord, modelGrid = getInterpModels(interpolatedDimensions, SQL,
boundaryValues, deckShape)
# If there are no grid points to interpolate between then no interpolation is necessary
if len(modelGridCoord) == 0: return modelGrid[0]
# Update our grid point based on interpolatedDimensions
gridPoint = []
for interpolatedDimension in interpolatedDimensions:
gridPoint.append(gridSpace[interpolatedDimension])
#pdb.set_trace()
#if len(interpolatedDimension) = 1 we have a oned interpolate
#griddate gives back nan values if that is not sorted. sent message to scipy mailing list
if len(interpolatedDimensions) == 1:
modelGrid = [modelGrid[i] for i in np.argsort(modelGridCoord)]
modelGridCoord = np.sort(modelGridCoord)
# Return the interpolated grid deck
#Fix for griddata scipy 0.9RC1 inspect this at a later time!!!
gridPoint = np.array(gridPoint).reshape(1, len(gridPoint))
#if modelGridCoord.ndim == 1: modelGridCoord = [modelGridCoord]
return interpolate.griddata(modelGridCoord,
modelGrid,
gridPoint,
method=method)
def getNearestNeighbours(model, Teff, logg, FeH, k=2.0, alpha=0.0, level=1):
"""
Finds the nearest neighbours to a point in a multi-dimensional grid.
Parameters:
===========
FeH : float
The metallicity ([Fe/H]) of the star you plan to interpolate for.
Teff : float
The effective temperature (Teff in Kelvin) of the star you plan to interpolate for.
logg : float
The surface gravity (log g) of the star you plan to interpolate for.
k : float, optional
The turbulence in the atmosphere of the star (km/s).
level : integer, optional
The maximum number of levels on either side of the point you wish to return in each
dimension.
"""
if (1 > level): raise ValueError, 'level must be a positive integer'
if (Teff < 0): raise ValueError, 'Teff must be a positive float'
if (logg < 0): raise ValueError, 'logg must be a positive float'
if (k < 0): raise ValueError, 'k must be a positive float'
connection = modeldb.getModelDBConn()
modelID = connection.execute(
'select id from atmosphy_conf '
'where model_name = ?', (model, )).fetchone()[0]
result = connection.execute(
'select Teff, logg, FeH, k, alpha from models'
' where model_id = ?', (modelID, ))
# todo - consider rewriting following section into a loop?
Teff_grid, logg_grid, FeH_grid, k_grid, alpha_grid = zip(
*result.fetchall())
connection.close()
grid = zip(Teff_grid, logg_grid, FeH_grid, k_grid, alpha_grid)
# Find the nearest N levels of indexedFeHs
FeH_neighbours = get1Dneighbours(FeH_grid, FeH, level=level)
# Find the Teff available for our FeH possibilites
Teff_available = [point[0] for point in grid if point[2] in FeH_neighbours]
Teff_neighbours = get1Dneighbours(Teff_available, Teff, level=level)
# Find the logg available for our FeH and Teff possibilities
logg_available = [
point[1] for point in grid
if point[2] in FeH_neighbours and point[0] in Teff_neighbours
]
logg_neighbours = get1Dneighbours(logg_available, logg, level=level)
# Find the k available for our FeH, Teff, and logg restricted
k_available = [
point[3] for point in grid if point[2] in FeH_neighbours
and point[0] in Teff_neighbours and point[1] in logg_neighbours
]
k_neighbours = get1Dneighbours(k_available, k, level=level)
# Find the alpha available for our FeH, Teff, logg, and k restricted
alpha_available = [
point[4] for point in grid
if point[2] in FeH_neighbours and point[0] in Teff_neighbours
and point[1] in logg_neighbours and point[3] in k_neighbours
]
alpha_neighbours = get1Dneighbours(alpha_available, alpha, level=level)
# Build the dimensions we want back from the SQL table
SQL = 'from models where MODEL_ID=%d and ' % modelID
boundaryValues = []
interpolatedDimensions = []
availableDimensions = {
'feh': FeH_neighbours,
'teff': Teff_neighbours,
'logg': logg_neighbours,
'k': k_neighbours,
'alpha': alpha_neighbours,
}
for dimension, value in zip(['teff', 'logg', 'feh', 'k', 'alpha'],
[Teff, logg, FeH, k, alpha]):
neighbours = availableDimensions[dimension]
# If only one 'neighbour' is present, then this dimension does not need to be interpolated upon
if (len(neighbours) > 1):
interpolatedDimensions.append(dimension)
# Add these limits for the sql query
boundaryValues.append(min(neighbours))
boundaryValues.append(max(neighbours))
SQL += ' %s between ? and ? and' % dimension
else:
boundaryValues.append(value)
SQL += ' %s = ? and' % dimension
if SQL[-3:] == 'and': SQL = SQL[:-3]
# Return the SQL
return (interpolatedDimensions, SQL, tuple(boundaryValues))
def interpModelGrid(modelName, Teff, logg, FeH, k=2.0, alpha=0.0, level=1, method='linear'):
"""
Interpolates in N-dimensional space to find the given point
(Teff, logg, FeH, k, alpha) given the model name.
Parameters:
===========
modelName : string
The name of the model to lookup in your local SQL database.
Teff : float
The effective temperature (Teff in Kelvin) of the star you plan to interpolate for.
FeH : float
The metallicity ([Fe/H]) of the star you plan to interpolate for.
logg : float
The surface gravity (log g) of the star you plan to interpolate for.
k : float, optional (default = 2.0)
The turbulence in the atmosphere of the star (km/s).
alpha : float, optional (default = 0.0)
The level of alpha enhancement of the star ([alpha/Fe] in dex).
level : integer, optional (default = 1)
The maximum number of levels on either side of the point you wish to return in each
dimension.
method : string, optional (default = 'linear')
The interpolation method which is passed to scipy.interpolate.griddata.
Options are 'linear', 'nearest', or 'cubic'.
"""
# Our grid point in N dimensionsal space
gridSpace = {
'teff' : Teff,
'logg' : logg,
'feh' : FeH,
'k' : k,
'alpha': alpha
}
conn = modeldb.getModelDBConn()
# Find the nearest neighbours in N dimensions, and get the SQL
interpolatedDimensions, SQL, boundaryValues = getNearestNeighbours(modelName, Teff, logg, FeH, k, alpha, level=level)
# Populate the model grid
deckShape = conn.execute('select ROWS, COLS from ATMOSPHY_CONF where MODEL_NAME=?', (modelName,)).fetchone()
modelGridCoord, modelGrid = getInterpModels(interpolatedDimensions, SQL, boundaryValues, deckShape)
# If there are no grid points to interpolate between then no interpolation is necessary
if len(modelGridCoord) == 0: return modelGrid[0]
# Update our grid point based on interpolatedDimensions
gridPoint = []
for interpolatedDimension in interpolatedDimensions:
gridPoint.append(gridSpace[interpolatedDimension])
#pdb.set_trace()
#if len(interpolatedDimension) = 1 we have a oned interpolate
#griddate gives back nan values if that is not sorted. sent message to scipy mailing list
if len(interpolatedDimensions) == 1:
modelGrid= [modelGrid[i] for i in np.argsort(modelGridCoord)]
modelGridCoord = np.sort(modelGridCoord)
# Return the interpolated grid deck
#Fix for griddata scipy 0.9RC1 inspect this at a later time!!!
gridPoint = np.array(gridPoint).reshape(1, len(gridPoint))
#if modelGridCoord.ndim == 1: modelGridCoord = [modelGridCoord]
return interpolate.griddata(modelGridCoord, modelGrid, gridPoint, method=method)
def getNearestNeighbours(model, Teff, logg, FeH, k=2.0, alpha=0.0, level=1):
"""
Finds the nearest neighbours to a point in a multi-dimensional grid.
Parameters:
===========
FeH : float
The metallicity ([Fe/H]) of the star you plan to interpolate for.
Teff : float
The effective temperature (Teff in Kelvin) of the star you plan to interpolate for.
logg : float
The surface gravity (log g) of the star you plan to interpolate for.
k : float, optional
The turbulence in the atmosphere of the star (km/s).
level : integer, optional
The maximum number of levels on either side of the point you wish to return in each
dimension.
"""
if (1 > level): raise ValueError, 'level must be a positive integer'
if (Teff < 0): raise ValueError, 'Teff must be a positive float'
if (logg < 0): raise ValueError, 'logg must be a positive float'
if (k < 0): raise ValueError, 'k must be a positive float'
connection = modeldb.getModelDBConn()
modelID = connection.execute('select id from atmosphy_conf '
'where model_name = ?', (model,)).fetchone()[0]
result = connection.execute('select Teff, logg, FeH, k, alpha from models'
' where model_id = ?', (modelID,))
# todo - consider rewriting following section into a loop?
Teff_grid, logg_grid, FeH_grid, k_grid, alpha_grid = zip(*result.fetchall())
connection.close()
grid = zip(Teff_grid, logg_grid, FeH_grid, k_grid, alpha_grid)
# Find the nearest N levels of indexedFeHs
FeH_neighbours = get1Dneighbours(FeH_grid, FeH, level=level)
# Find the Teff available for our FeH possibilites
Teff_available = [point[0] for point in grid if point[2] in FeH_neighbours]
Teff_neighbours = get1Dneighbours(Teff_available, Teff, level=level)
# Find the logg available for our FeH and Teff possibilities
logg_available = [point[1] for point in grid if point[2] in FeH_neighbours and point[0] in Teff_neighbours]
logg_neighbours = get1Dneighbours(logg_available, logg, level=level)
# Find the k available for our FeH, Teff, and logg restricted
k_available = [point[3] for point in grid if point[2] in FeH_neighbours and point[0] in Teff_neighbours and point[1] in logg_neighbours]
k_neighbours = get1Dneighbours(k_available, k, level=level)
# Find the alpha available for our FeH, Teff, logg, and k restricted
alpha_available = [point[4] for point in grid if point[2] in FeH_neighbours and point[0] in Teff_neighbours and point[1] in logg_neighbours and point[3] in k_neighbours]
alpha_neighbours = get1Dneighbours(alpha_available, alpha, level=level)
# Build the dimensions we want back from the SQL table
SQL = 'from models where MODEL_ID=%d and ' % modelID
boundaryValues = []
interpolatedDimensions = []
availableDimensions = {
'feh' : FeH_neighbours,
'teff' : Teff_neighbours,
'logg' : logg_neighbours,
'k' : k_neighbours,
'alpha' : alpha_neighbours,
}
for dimension, value in zip(['teff', 'logg', 'feh', 'k', 'alpha'], [Teff, logg, FeH, k, alpha]):
neighbours = availableDimensions[dimension]
# If only one 'neighbour' is present, then this dimension does not need to be interpolated upon
if (len(neighbours) > 1):
interpolatedDimensions.append(dimension)
# Add these limits for the sql query
boundaryValues.append(min(neighbours))
boundaryValues.append(max(neighbours))
SQL += ' %s between ? and ? and' % dimension
else:
boundaryValues.append(value)
SQL += ' %s = ? and' % dimension
if SQL[-3:] == 'and': SQL = SQL[:-3]
# Return the SQL
return (interpolatedDimensions, SQL, tuple(boundaryValues))