def test_no_wl_truncation(self, mock_no_alpha_grid, mock_instrument,
tmpdir_factory):
tmpdir = tmpdir_factory.mktemp("hdf5tests")
outfile = tmpdir.join("test_no_instrument.hdf5")
creator = HDF5Creator(mock_no_alpha_grid,
filename=outfile,
instrument=None,
wl_range=None)
np.testing.assert_array_almost_equal_nulp(creator.wl_final,
mock_no_alpha_grid.wl[1:-1])
def test_invalid_wavelengths(self, wl_range, mock_no_alpha_grid,
mock_instrument, tmpdir_factory):
tmpdir = tmpdir_factory.mktemp("hdf5tests")
outfile = tmpdir.join("test_no_instrument.hdf5")
with pytest.raises(ValueError):
HDF5Creator(
mock_no_alpha_grid,
filename=outfile,
instrument=mock_instrument,
wl_range=wl_range,
)
def mock_creator(mock_no_alpha_grid, mock_instrument, tmpdir_factory,
grid_points):
ranges = np.vstack([np.min(grid_points, 0), np.max(grid_points, 0)]).T
tmpdir = tmpdir_factory.mktemp("hdf5tests")
outfile = tmpdir.join("test_grid.hdf5")
creator = HDF5Creator(
mock_no_alpha_grid,
filename=outfile,
instrument=mock_instrument,
wl_range=(2e4, 3e4),
ranges=ranges,
)
yield creator
def test_no_instrument(self, mock_no_alpha_grid, tmpdir_factory,
grid_points):
ranges = np.vstack([np.min(grid_points, 0), np.max(grid_points, 0)]).T
tmpdir = tmpdir_factory.mktemp("hdf5tests")
outfile = tmpdir.join("test_no_instrument.hdf5")
creator = HDF5Creator(
mock_no_alpha_grid,
filename=outfile,
instrument=None,
wl_range=(2e4, 3e4),
ranges=ranges,
)
creator.process_grid()
def test_no_par_truncation(self, mock_no_alpha_grid, mock_instrument,
tmpdir_factory):
tmpdir = tmpdir_factory.mktemp("hdf5tests")
outfile = tmpdir.join("test_no_instrument.hdf5")
creator = HDF5Creator(
mock_no_alpha_grid,
filename=outfile,
instrument=mock_instrument,
ranges=None,
)
for cpars, gpars in zip(creator.points,
np.asarray(mock_no_alpha_grid.points).T):
np.testing.assert_allclose(cpars, np.unique(gpars))
def test_par_truncation(self, grid_points, mock_no_alpha_grid,
mock_instrument, tmpdir_factory):
tmpdir = tmpdir_factory.mktemp("hdf5tests")
outfile = tmpdir.join("test.hdf5")
ranges = [(6000, 6200), (4.0, 5.0), (-1.0, 0.0)]
creator = HDF5Creator(
mock_no_alpha_grid,
filename=outfile,
instrument=mock_instrument,
ranges=ranges,
)
for cpars, gpars in zip(creator.points, grid_points.T):
np.testing.assert_allclose(cpars, np.unique(gpars))
def test_wavelength_truncation(self, wl_range, wl_expected,
mock_no_alpha_grid, mock_instrument,
tmpdir_factory):
tmpdir = tmpdir_factory.mktemp("hdf5tests")
outfile = tmpdir.join("test_no_instrument.hdf5")
creator = HDF5Creator(
mock_no_alpha_grid,
filename=outfile,
instrument=mock_instrument,
wl_range=wl_range,
)
np.testing.assert_array_almost_equal_nulp(creator.wl_final[0],
wl_expected[0], 3)
np.testing.assert_array_almost_equal_nulp(creator.wl_final[-1],
wl_expected[-1], 3)
name="CRIRES",
FWHM=fwhm,
wl_range=Starfish.grid["wl_range"]):
super().__init__(name=name, FWHM=FWHM, wl_range=wl_range)
# Sets the FWHM and wl_range
# In[ ]:
mygrid = BTSETTL(norm=False, air=False, base=Starfish.grid["btsettle_raw"]
) # Disable normalization to solar boloametic flux.
instrument = CRIRES_50k()
# HDF5Creator(GridInterface, filename, Instrument, ranges=None, key_name='t{0:.0f}g{1:.1f}', vsinis=None)
# Specify hdf5_path in config.yaml file.
creator = HDF5Creator(mygrid,
Starfish.grid["btsettle_hdf5_path"],
instrument,
ranges=Starfish.grid["parrange"])
# Need to change starfish BT-SETTL to change how it handles param_names and points
# Might need own interface as there is hardcoded folder CXXXX2011
# In[ ]:
creator.process_grid()
# # Loading BTSETTL Directly
# In[ ]:
from Starfish.grid_tools import load_BTSettl
wl_range=Starfish.grid["wl_range"]):
super().__init__(name=name, FWHM=FWHM, wl_range=wl_range)
# Sets the FWHM and wl_range
print(CRIRES_50k())
# Process the grid and save to the hdf5 file.
mygrid = PHOENIX(norm=False,
air=False) # Disable normalization to solar boloametic flux.
instrument = CRIRES_50k()
# HDF5Creator(GridInterface, filename, Instrument, ranges=None, key_name='t{0:.0f}g{1:.1f}', vsinis=None)
# Specify hdf5_path in config.yaml file.
creator = HDF5Creator(
mygrid,
"/home/jneal/Phd/Codes/companion_simulations/starfish_tests/libraries/PHOENIX_50k.hdf5",
instrument,
ranges=Starfish.grid["parrange"])
creator.process_grid()
mygrid = PHOENIX(norm=False,
air=True) # Disable normalization to solar boloametic flux.
creator = HDF5Creator(
mygrid,
"/home/jneal/Phd/Codes/companion_simulations/starfish_tests/libraries/PHOENIX_air.hdf5",
instrument,
ranges=Starfish.grid["parrange"])
creator.process_grid()
ranges = [[5700, 8600], [4.0, 6.0], [-0.5, 0.5]]
download_PHOENIX_models(path="PHOENIX", ranges=ranges)
#%%
# Setup a grid interface with the models
from Starfish.grid_tools import PHOENIXGridInterfaceNoAlpha
grid = PHOENIXGridInterfaceNoAlpha(path="PHOENIX")
# Setup an HDF5 interface in order to allow much quicker reading and writing
# than compared to loading FITS files over and over again.
from Starfish.grid_tools.instruments import SPEX
from Starfish.grid_tools import HDF5Creator
creator = HDF5Creator(grid,
"F_SPEX_grid.hdf5",
instrument=SPEX(),
wl_range=(0.9e4, np.inf),
ranges=ranges)
creator.process_grid()
#%%
# use the HDF5 Interface to consrtuct the spectral emulator
from Starfish.emulator import Emulator
emu = Emulator.from_grid("F_SPEX_grid.hdf5")
print(emu)
#%%
# train the emulator (PCA)
emu.train(options=dict(maxiter=1e5))
from Starfish.grid_tools import PHOENIXGridInterface, HDF5Creator, TRES
raw_library_path = "../../libraries/raw/PHOENIX/"
mygrid = PHOENIXGridInterface(base=raw_library_path, wl_range=[4700, 5500])
out_path = "../../libraries/" + "PHOENIX_F.hdf5"
instrument = TRES()
# Limit the range of stellar parameters correspondi to an F star
creator = HDF5Creator(mygrid, out_path, instrument,
ranges={"temp":(5800, 6500), "logg":(3.5,6.0),
"Z":(-1.5,1.0), "alpha":(0.0,0.0)})
creator.process_grid()
#%%
# Setup a grid interface with the models
from Starfish.grid_tools import PHOENIXGridInterfaceNoAlpha
grid = PHOENIXGridInterfaceNoAlpha(path="PHOENIX")
# Setup an HDF5 interface in order to allow much quicker reading and writing
# than compared to loading FITS files over and over again.
from Starfish.grid_tools.instruments import IGRINS_H_custom
from Starfish.grid_tools import HDF5Creator
creator = HDF5Creator(
grid, "IGRINS_grid.hdf5",instrument=IGRINS_H_custom(),
wl_range=(16600, 16700), ranges=ranges)
creator.process_grid()
#%%
from Starfish.emulator import Emulator
emu = Emulator.from_grid("IGRINS_grid.hdf5")
print(emu)
#%%
emu.train(options=dict(maxiter=1e5))
print(emu)
"New in v0.3: Using explicit air/vacuum state from Instrument class."
)
except AttributeError:
air = True
if (Starfish.data["grid_name"] == "PHOENIX") & (len(
Starfish.grid['parname']) == 3):
mygrid = eval("Starfish.grid_tools." + Starfish.data["grid_name"] +
"GridInterfaceNoAlpha")(air=air)
else:
mygrid = eval("Starfish.grid_tools." + Starfish.data["grid_name"] +
"GridInterface")(air=air)
hdf5_path = os.path.expandvars(Starfish.grid["hdf5_path"])
creator = HDF5Creator(mygrid,
hdf5_path,
instrument,
ranges=Starfish.grid["parrange"])
creator.process_grid()
if args.plot:
# Check to make sure the file exists
import os
hdf5_path = os.path.expandvars(Starfish.grid["hdf5_path"])
if not os.path.exists(hdf5_path):
print(
"HDF5 file does not yet exist. Please run `grid.py create` first.")
import sys
sys.exit()
"New in v0.3: Using explicit air/vacuum state from Instrument class."
)
except AttributeError:
air = True
if (Starfish.data["grid_name"] == "PHOENIX") & (len(
Starfish.grid['parname']) == 3):
mygrid = eval("Starfish.grid_tools." + Starfish.data["grid_name"] +
"GridInterfaceNoAlpha")(air=air)
else:
mygrid = eval("Starfish.grid_tools." + Starfish.data["grid_name"] +
"GridInterface")(air=air)
hdf5_path = os.path.expandvars(Starfish.grid["hdf5_path"])
creator = HDF5Creator(mygrid,
hdf5_path,
instrument,
ranges=Starfish.grid["parrange"])
creator.process_grid()
if args.plot:
# Check to make sure the file exists
import os
hdf5_path = os.path.expandvars(Starfish.grid["hdf5_path"])
if not os.path.exists(hdf5_path):
print(
"HDF5 file does not yet exist. Please run `grid.py create` first.")
import sys
sys.exit()