def example_db():
"""
Simplistic database with one molecule
with same resolution for all wavelength
"""
data = config.Configuration("Example_db.cfg")
molecule_data = data["Molecule"]
outpath = Example_DB
db_name = "cross_sec_Example.db"
user = "******"
db_info = [outpath, db_name, user]
numin = 3000
numax = 4000
step = 10
method = "Voigt"
source = "HITRAN_LL"
T_grid = [250, 300, 350]
P_grid = [100000, 10000, 1000]
gamma = "gamma_self"
cross = True
db_init = csdb.xsec_generator(db_info, numin, numax, step, method, source)
for molecule in molecule_data:
component = np.array(molecule_data[molecule]["component"],
dtype=np.int)
d_path = os.path.join(HITRAN_Lines, molecule)
db_init.single_molecule_inject(d_path, molecule, component, gamma,
cross, P_grid, T_grid)
def exomol_db2():
"""
Simplistic database with one molecule
with same resolution for all wavelength
"""
user_input = config.Configuration(
"../../bin_stable/a.Main/user_input_dev.cfg")
molecule = "31P-1H3"
outpath = Exomol_DB
db_name = "Exomol_PH3.db"
user = "******"
db_info = [outpath, db_name, user]
numin = 400
numax = 9999
step = 1
method = "Doppler"
source = "Exomol"
T_grid = user_input["Simulation_Control"]["T_Grid"]
P_grid = user_input["Simulation_Control"]["P_Grid"]
db_init = csdb.xsec_generator(db_info, numin, numax, step, method, source)
d_path = os.path.join(Exomol_Xsec, molecule)
print d_path
db_init.exomol_inject2(d_path, "PH3", P_grid, T_grid)
def demo_db():
data = config.Configuration("Demo_db.cfg")
molecule_data = data["Molecule"]
outpath = Demo_DB
db_name = "cross_sec_Demo.db"
user = "******"
db_info = [outpath, db_name, user]
numin = 400
numax = 30000
step = 10
method = "Voigt"
source = "HITRAN_LL"
T_grid = [200,300,400,500,600,700,800]
P_grid = [100000.0, 36800.0, 13500.0, 4980.0, 1830.0, 674.0, 248.0, 91.2, 33.5, 12.3, 4.54, 1.67, 0.614, 0.226, 0.0832, 0.0306, 0.0113, 0.00414, 0.00152]
gamma = "gamma_self"
cross = True
db_init = csdb.xsec_generator(db_info,numin,numax,step,method,source)
for molecule in molecule_data:
component = np.array(molecule_data[molecule]["component"],dtype=np.int)
d_path = os.path.join(HITRAN_Lines,molecule)
db_init.single_molecule_inject(d_path,molecule,component,gamma,cross,P_grid,T_grid)
def db_load():
inputs = config.Configuration("../../bin_stable/a.Main/user_input_dev.cfg")
molecule = "PH3"
kwargs = {
"dir": Exomol_DB,
"db_name": "Exomol_PH3.db",
"user": "******",
"DEBUG": False,
"REMOVE": True,
"BACKUP": False,
"OVERWRITE": True
}
cross_db = dbm.database(**kwargs)
cross_db.access_db()
result = cross_db.c.execute(
"SELECT nu, coef FROM {} WHERE P={} AND T={} AND nu>={} AND nu<={} ORDER BY nu"
.format(molecule, 13500.0, 300, 400, 9999))
fetch = np.array(result.fetchall()).T
nu = fetch[0]
coef = fetch[1]
plotter = Plotter()
plotter.plot_xy(10000. / nu, coef)
def db_load_bulk():
inputs = config.Configuration("../../bin_stable/a.Main/user_input_dev.cfg")
molecule = "PH3"
kwargs = {
"dir": Exomol_DB,
"db_name": "Exomol_PH3.db",
"user": "******",
"DEBUG": False,
"REMOVE": True,
"BACKUP": False,
"OVERWRITE": True
}
cross_db = dbm.database(**kwargs)
cross_db.access_db()
nu, data = exomol_cross_section_loader(inputs, cross_db, molecule)
print len(nu)
plt_ref_1 = sim_plot.plot_xy(s.nu, s.normalized_stellar_spectra,
"Stellar Spectra")
plt_ref_2 = sim_plot.plot_xy(
s.nu, s.normalized_stellar_spectra * s.Reference_Reflect_Signal,
"Reflection Spectra")
sim_plot.set_legend([plt_ref_1, plt_ref_2])
if utils.to_bool(user_input["Save"]["Plot"]["save"]):
sim_plot.save_plot()
else:
sim_plot.show_plot()
if __name__ == "__main__":
user_input = config.Configuration(
"../../bin_stable/a.Main/user_input_dev.cfg")
user_input["Simulation_Control"]["DB_DIR"] = "Example"
user_input["Simulation_Control"]["DB_Name"] = "cross_sec_Example.db"
user_input["Simulation_Control"]["TP_Profile_Name"] = "isothermal_300K.txt"
user_input["Simulation_Control"]["Mixing_Ratio_Name"] = "H2O_only.txt"
user_input["Save"]["Plot"]["save"] = False
user_input["Save"]["Intermediate_Data"][
"cross_section_savename"] = "Temp_H2O_Cross_Section.npy"
simulation = theory.RS_Simulator(user_input)
observer = observe.OS_Simulator(user_input)
analyzer = analyze.Spectra_Analyzer(user_input)
simulate(simulation, observer, analyzer)
import os
import sys
import numpy as np
DIR = os.path.abspath(os.path.dirname(__file__))
sys.path.insert(0, os.path.join(DIR, '../..'))
import SEAS_Utils.common_utils.configurable as config
from SEAS_Utils.common_utils.DIRs import TP_Profile_Data
from SEAS_Utils.common_utils.data_loader import two_column_file_loader
import SEAS_Utils.common_utils.data_plotter as plt
if __name__ == "__main__":
user_input = config.Configuration("user_input_dev.cfg")
if user_input["Simulation_Control"]["TP_Profile"] == "File":
filename = os.path.join(TP_Profile_Data,user_input["Simulation_Control"]["TP_Profile_Name"])
x,y = two_column_file_loader(filename)
plt.simple_plot(y,np.log10(x))
import os
import sys
import numpy as np
DIR = os.path.abspath(os.path.dirname(__file__))
sys.path.insert(0, os.path.join(DIR, '../..'))
import SEAS_Utils.common_utils.configurable as config
from SEAS_Utils.common_utils.DIRs import Mixing_Ratio_Data
from SEAS_Utils.common_utils.data_loader import multi_column_file_loader
import SEAS_Utils.common_utils.data_plotter as plt
if __name__ == "__main__":
user_input = config.Configuration("../a.Main/user_input_dev.cfg")
if user_input["Simulation_Control"]["Mixing_Ratio"] == "File":
filename = os.path.join(Mixing_Ratio_Data,user_input["Simulation_Control"]["Mixing_Ratio_Name"])
print filename
data = multi_column_file_loader(filename,type="mixed")
pressure = data[0]
mixing_ratio = data[1:]
print pressure
print mixing_ratio
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
This code test the generation of TP Profiles
"""
import os
import sys
DIR = os.path.abspath(os.path.dirname(__file__))
sys.path.insert(0, os.path.join(DIR, '../..'))
import SEAS_Aux.atmosphere_processes.TP_profile_generator as TPgen
import SEAS_Utils.common_utils.configurable as config
if __name__ == "__main__":
TP_input = config.Configuration(
"TP_selection.cfg")["Test Isothermal Atmosphere"]
simulator = TPgen.temperature_pressure_profile_generator(
TP_input, name="isothermal_300K.txt")
simulator.generate()
simulator.save()
s.nu_window = a.spectra_window(nu, ref_trans, "T", 0.3, 100., s.min_signal)
sim_plot.plot_window(s.nu_window, "k", 0.2)
sim_plot.set_legend(plt_legend)
sim_plot.show_plot()
return s
if __name__ == "__main__":
Timer = simple_timer()
user_input = config.Configuration(
os.path.join(track, "bin_stable/a.Main/user_input_dev.cfg"))
Filename = "Test_Earth"
Filename1 = "Test_Earth_with_biosig"
user_input["Simulation_Control"]["DB_DIR"] = "Simulation_Band"
user_input["Simulation_Control"]["DB_Name"] = None #"cross_sec_Example.db"
user_input["Simulation_Control"]["TP_Profile_Name"] = "earth.txt"
user_input["Simulation_Control"]["Mixing_Ratio_Name"] = "earth.txt"
user_input["Save"]["Intermediate_Data"][
"cross_section_savename"] = "%s_Cross_Section.npy" % Filename
user_input["Save"]["Window"]["path"] = os.path.join(
track, "output/Simple_Atmosphere_Window")
user_input["Save"]["Window"][
"name"] = "%s_Window_A1000_S100.txt" % Filename1
def generate_water():
ratio_input = config.Configuration("water_only_selection.cfg")
simulator = mix.mixing_ratio_generator(ratio_input,filler=False,name="selection/water_only2.txt")
simulator.generate()
simulator.save()
DIR = os.path.abspath(os.path.dirname(__file__))
sys.path.insert(0, os.path.join(DIR, '../..'))
import SEAS_Aux.atmosphere_processes.mixing_ratio_generator as mix
import SEAS_Utils.common_utils.configurable as config
def generate_water():
ratio_input = config.Configuration("water_only_selection.cfg")
simulator = mix.mixing_ratio_generator(ratio_input,filler=False,name="selection/water_only2.txt")
simulator.generate()
simulator.save()
if __name__ == "__main__":
ratio_input = config.Configuration("selection/h2_only_selection.cfg")
simulator = mix.mixing_ratio_generator(ratio_input,
filler=True,
filler_molecule="He",
pressures = [100000.0, 36800.0, 13500.0, 4980.0, 1830.0, 674.0, 248.0, 91.2, 33.5, 12.3, 4.54, 1.67, 0.614, 0.226, 0.0832, 0.0306, 0.0113, 0.00414, 0.00152, 0.00056, 0.000206, 7.58e-05, 2.79e-05, 1.03e-05],
name="H2&He.txt",
overwrite=True)
simulator.generate()
simulator.save()
x1, y1 = load_NIST_spectra(smiles, ["wn", "A"], True)
y2 = biosig_interpolate(x1, y1, nu, "A")
leg2, = plt.plot(10000. / nu, np.array(y2), label="NIST")
legends = [leg1, leg2]
plt.legend(handles=legends)
plt.xlabel("Wavenumber (cm^-1)")
plt.ylabel("Absorption (proxy)")
plt.title('Simulated ATMOS vs NIST Molecular Absorption for: %s' % smiles)
plt.show()
if __name__ == "__main__":
molecule_input = config.Configuration("atmos_data.cfg")
window = "earth2_atmosphere"
pressure = 10e6
temperature = 300
for smiles in molecule_input:
Simulator = ATMOS_1_Simulator(smiles, window, pressure, temperature)
nu = np.arange(400, 30000, 1)
xsec = Simulator.get_cross_section(nu)
leg1, = plt.plot(10000. / nu, xsec, label="ATMOS")
x1, y1 = load_NIST_spectra(smiles, ["wn", "A"], True)
y2 = biosig_interpolate(x1, y1, nu, "A")
leg2, = plt.plot(10000. / nu, np.array(y2), label="NIST")
