def test_4_upload_to_public(self):
if self.put.private_key is not None:
download = GetData(data_path_name=self.PRIVATE_DOWNLOAD_TEST)
self.put.to_server(self.PRIVATE_DOWNLOAD_TEST,
server_path=self.UPLOAD_TEST,
server_type='public')
self.assertTrue(
self.put.check_private_server_data_path(
self.put.server_public_write_access_path),
msg='Public upload test file expected to be located at: ' +
self.put.server_public_write_access_path)
def _update_xml_beamlet_source(xml_file, h5_path):
param = GetData(data_path_name=xml_file).data
param.getroot().find('body').find('beamlet_source').text = h5_path
param.write('data/' + xml_file)
class BeamletFromIds:
def __init__(self, input_source='beamlet/test_imas.xml'):
self.access_path = input_source
self.read_imas_xml()
self.machine = self.param.getroot().find('body').find(
'imas_machine').text
self.user = self.param.getroot().find('body').find('imas_user').text
self.shotnumber = int(
self.param.getroot().find('body').find('imas_shotnumber').text)
self.runnumber = int(
self.param.getroot().find('body').find('imas_runnumber').text)
self.timeslice = float(
self.param.getroot().find('body').find('imas_timeslice').text)
self.profile_source = self.param.getroot().find('body').find(
'profile_source').text
self.load_imas_profiles()
self.equilibrium_source = self.param.getroot().find('body').find(
'device_magnetic_geometry').text
self.load_imas_equilibrium()
self.get_beamlet_current(current=0.002)
self.get_beamlet_energy(energy=60)
self.get_beamlet_species(species='Li')
self.beamlet_profile_configuration()
def read_imas_xml(self):
self.param = GetData(data_path_name=self.access_path).data
assert isinstance(self.param, etree._ElementTree)
print('ElementTree read to dictionary from: ' + self.access_path)
def get_beamlet_energy(self, energy=None):
if (energy is not None) and (isinstance(energy, int)):
beamlet_energy = etree.SubElement(
self.param.getroot().find('body'),
'beamlet_energy',
unit='keV')
beamlet_energy.text = str(energy)
else:
print(
'Further data exploitation development is in process. Currently beam energy to be added manually'
)
raise Exception('Missing beam energy input.')
def get_beamlet_current(self, current=None):
if (current is not None) and (isinstance(current, float)):
beamlet_current = etree.SubElement(
self.param.getroot().find('body'), 'beamlet_current', unit='A')
beamlet_current.text = str(current)
else:
print(
'Further data exploitation development is in process. Currently beam current to be added manually'
)
raise Exception('Missisng beam current input.')
def get_beamlet_species(self, species=None):
if (species is not None) and (isinstance(species, str)):
beamlet_species = etree.SubElement(
self.param.getroot().find('body'), 'beamlet_species', unit='')
beamlet_species.text = str(species)
else:
print(
'Further data exploitation development is in process. Currently beam species to be added manually'
)
raise Exception('Missisng beam species input.')
def get_beamlet_ends(self):
start = [
float(self.param.getroot().find('body').find('beamlet_start').find(
'x').text),
float(self.param.getroot().find('body').find('beamlet_start').find(
'y').text),
float(self.param.getroot().find('body').find('beamlet_start').find(
'z').text)
]
end = [
float(self.param.getroot().find('body').find('beamlet_end').find(
'x').text),
float(self.param.getroot().find('body').find('beamlet_end').find(
'y').text),
float(self.param.getroot().find('body').find('beamlet_end').find(
'z').text)
]
return np.asarray(start), np.asarray(end)
def load_imas_profiles(self):
if self.profile_source == 'core_profiles':
self.run_prof = ProfilesIds(self.shotnumber, self.runnumber,
self.profile_source)
else:
print('There is no input protocol for data stored in ' +
self.profile_source + ' IDS')
raise Exception(
'The requested IDS does not exist or data fetch for it is not implemented'
)
def load_imas_equilibrium(self):
if self.equilibrium_source == 'equilibrium':
self.equilibrium = EquilibriumIds(self.shotnumber, self.runnumber)
else:
print('There is no input protocol for data stored in ' +
self.equilibrium_source + ' IDS')
raise Exception(
'The requested IDS does not exist or data fetch for it is not implemented'
)
def beamlet_profile_configuration(self):
ids_density = self.run_prof.get_electron_density(self.timeslice)
ids_electron_temperature = self.run_prof.get_electron_temperature(
self.timeslice)
ids_ion_temperature = self.run_prof.get_ion_temperature(self.timeslice)
ids_grid = self.run_prof.get_grid_in_psi(
self.timeslice) / self.run_prof.get_grid_in_psi(self.timeslice)[-1]
f_density = interp1d(ids_grid, ids_density)
f_ion_temp = interp1d(ids_grid, ids_ion_temperature)
f_electron_temp = interp1d(ids_grid, ids_electron_temperature)
resolution = int(
self.param.getroot().find('body').find('beamlet_resolution').text)
start, end = self.get_beamlet_ends()
beamlet_gird = np.linspace(0, uc.distance(start, end), resolution)
beamlet_flux = self.beamlet_grid_psi(beamlet_gird, start,
uc.unit_vector(start, end))
beamlet_density = np.concatenate(
(self.profile_extrapol(beamlet_flux[np.where(beamlet_flux > 1)[0]],
[1, ids_density[-1]], [1.2, 1e+17]),
f_density(beamlet_flux[np.where(beamlet_flux <= 1)[0]])))
beamlet_electron_temp = np.concatenate(
(self.profile_extrapol(beamlet_flux[np.where(beamlet_flux > 1)[0]],
[1, ids_electron_temperature[-1]],
[1.2, 10]),
f_electron_temp(beamlet_flux[np.where(beamlet_flux <= 1)[0]])))
beamlet_ion_temp = np.concatenate(
(self.profile_extrapol(beamlet_flux[np.where(beamlet_flux > 1)[0]],
[1, ids_ion_temperature[-1]], [1.2, 5]),
f_ion_temp(beamlet_flux[np.where(beamlet_flux <= 1)[0]])))
self.profiles = pandas.DataFrame(
data={
'beamlet_density':
np.reshape(beamlet_density, beamlet_density.shape[0]),
'beamlet_electron_temp':
np.reshape(beamlet_electron_temp,
beamlet_electron_temp.shape[0]),
'beamlet_grid':
beamlet_gird,
'beamlet_ion_temp':
np.reshape(beamlet_ion_temp, beamlet_ion_temp.shape[0])
})
def beamlet_grid_psi(self, beamlet_gird, start, vector):
normalized_flux = self.equilibrium.get_normalized_2d_flux(
self.timeslice)
r_flux, z_flux = self.equilibrium.get_2d_equilibrium_grid(
self.timeslice)
flux_function = interp2d(r_flux, z_flux, normalized_flux, kind='cubic')
beamlet_flux = []
for distance in beamlet_gird:
point = uc.cartesian_to_cylin(start - distance * vector)
beamlet_flux.append(flux_function(point[0], point[1]))
return np.asarray(beamlet_flux)
def profile_extrapol(self, vector, boundary_point, reference_point):
b = np.log(boundary_point[1] / reference_point[1]) / (
boundary_point[0] - reference_point[0])
a = boundary_point[1] / np.exp(b * boundary_point[0])
return a * np.exp(b * vector)
def read_imas_xml(self):
self.param = GetData(data_path_name=self.access_path).data
assert isinstance(self.param, etree._ElementTree)
print('ElementTree read to dictionary from: ' + self.access_path)
def test_parentage(self):
self.data = GetData(self.PUBLIC_DOWNLOAD_TEST)
self.assertIsInstance(
self.data,
AccessData,
msg='The GetData object is expected to a child of AccessData.')