diff --git a/idstools/compute/summary.py b/idstools/compute/summary.py index 0847002b..f45277c4 100644 --- a/idstools/compute/summary.py +++ b/idstools/compute/summary.py @@ -90,7 +90,7 @@ def get_summary( # The `energy_mhd` variable in the `get_summary` method is used to retrieve the "energy_mhd" # waveform values from the `global_quantities` of the summary ids object. If the length of the # retrieved values is less than 1, it logs a critical error message indicating that the data - # could not be read and assigns an array of NaN values with the same length as the time vector + # could not be read and assigns an array of nan values with the same length as the time vector # to the `energy_mhd` variable. This ensures that the `energy_mhd` waveform data is handled # properly even in the case of missing or unreadable data. energy_mhd = self.ids.global_quantities.energy_mhd.value diff --git a/idstools/domain/ecstray.py b/idstools/domain/ecstray.py index 4824f9e4..0dec54fd 100644 --- a/idstools/domain/ecstray.py +++ b/idstools/domain/ecstray.py @@ -177,8 +177,8 @@ def get_cutoff_layer(self, coherent_wave_index, time_slice): ) + constants.e * b_total[ir, iz] / (2 * constants.m_e) except Exception as e: # Not defined outside LCFS logger.debug(f"{e}") - ne2d_eq[ir, iz] = -1 # np.NaN - omega_r[ir, iz] = -1 # np.NaN + ne2d_eq[ir, iz] = -1 # np.nan + omega_r[ir, iz] = -1 # np.nan # Find (R,Z) where omega_R = omega_EC (within the tolerance omega_err) [nr, nz] = np.shape(omega_r) diff --git a/idstools/domain/kineticprofiles.py b/idstools/domain/kineticprofiles.py index 80081501..6d39b90a 100644 --- a/idstools/domain/kineticprofiles.py +++ b/idstools/domain/kineticprofiles.py @@ -787,7 +787,7 @@ def get_zeff_profile(self): if len(_zeff) != self.nrho: logger.warning("core_profiles.profiles_1d[:].zeff could not be read.") logger.warning(f"Size mismatch: rho_tor_norm = {self.nrho}, " f"zeff = {len(_zeff)}") - _zeff = np.asarray([np.NaN] * self.nrho) + _zeff = np.asarray([np.nan] * self.nrho) for i in range(self.nrho): zeff[i] = _zeff[i] if self.is_edge_profiles_present: @@ -795,14 +795,14 @@ def get_zeff_profile(self): _zeff = self.edge_profiles.profiles_1d[self.time_index_edge_profiles].zeff.value if len(_zeff) < 1: logger.warning("edge_profiles.profiles_1d[:].zeff could not be read.") - _zeff = np.asarray([np.NaN] * self.erho) + _zeff = np.asarray([np.nan] * self.erho) for i in range(self.erho): zeff[self.nrho + i] = _zeff[i] else: _gset = self.edge_profiles.ggd[self.time_index_edge_profiles].zeff[self.gset].values if len(_gset) < 1: logger.warning("edge_profiles.ggd[:].zeff could not be read.") - _gset = np.asarray([np.NaN] * self.erho) + _gset = np.asarray([np.nan] * self.erho) for i in range(self.erho): zeff[self.nrho + i] = _gset[i] return zeff @@ -814,7 +814,7 @@ def getne_profile(self): Returns: The function `getne_profile` returns a list of electron density values. The electron density values are collected from different sources based on the conditions specified in the function. - The returned list contains electron density values for both core and edge profiles, with NaN + The returned list contains electron density values for both core and edge profiles, with nan values filled in case of missing data. """ electron_density = [0] * (self.nrho + self.erho) @@ -823,7 +823,7 @@ def getne_profile(self): if len(_density) != self.nrho: logger.warning("core_profiles.profiles_1d[:].electrons.density could not be read.") logger.warning(f"Size mismatch: rho_tor_norm = {self.nrho}, electrons.density =" f"{len(_density)}") - _density = np.asarray([np.NaN] * self.nrho) + _density = np.asarray([np.nan] * self.nrho) for i in range(self.nrho): electron_density[i] = _density[i] if self.is_edge_profiles_present: @@ -831,14 +831,14 @@ def getne_profile(self): _density = self.core_profiles.profiles_1d[self.time_index_edge_profiles].electrons.density.value if len(_density) < 1: logger.warning("edge_profiles.profiles_1d[:].electrons.density could not be read.") - _density = np.asarray([np.NaN] * self.erho) + _density = np.asarray([np.nan] * self.erho) for i in range(self.erho): electron_density[self.nrho + i] = _density[i] else: _gset = self.edge_profiles.ggd[self.time_index_edge_profiles].electrons.density[self.gset].values if len() < 1: logger.warning("edge_profiles.ggd[:].electrons.density could not be read.") - _gset = np.asarray([np.NaN] * self.erho) + _gset = np.asarray([np.nan] * self.erho) for i in range(self.erho): electron_density[self.nrho + i] = _gset[i] return electron_density @@ -862,7 +862,7 @@ def gette_profile(self): logger.warning( f"Size mismatch: rho_tor_norm = {self.nrho}, electrons.temperature = " f"{len(_temperature)}" ) - _temperature = np.asarray([np.NaN] * self.nrho) + _temperature = np.asarray([np.nan] * self.nrho) for i in range(self.nrho): electron_temperature[i] = _temperature[i] * 1.0e-3 if self.is_edge_profiles_present: @@ -870,14 +870,14 @@ def gette_profile(self): _temperature = self.edge_profiles.profiles_1d[self.time_index_edge_profiles].electrons.temperature if len(_temperature) < 1: logger.warning("edge_profiles.profiles_1d[:].electrons.temperature could not be read.") - _temperature = np.asarray([np.NaN] * self.erho) + _temperature = np.asarray([np.nan] * self.erho) for i in range(self.erho): electron_temperature[self.nrho + i] = _temperature[i] * 1.0e-3 else: _gset = self.edge_profiles.ggd[self.time_index_edge_profiles].electrons.temperature[self.gset].values if len() < 1: logger.warning("edge_profiles.ggd[:].electrons.temperature could not be read.") - _gset = np.asarray([np.NaN] * self.erho) + _gset = np.asarray([np.nan] * self.erho) for i in range(self.erho): electron_temperature[self.nrho + i] = _gset[i] * 1.0e-3 return electron_temperature @@ -897,7 +897,7 @@ def getti_flag(self): if len(t_i_average) != self.nrho: logger.warning("core_profiles.profiles_1d[:].t_i_average could not be read.") logger.warning(f"Size mismatch: rho_tor_norm = {self.nrho}, t_i_average = " f"{len(t_i_average)}") - t_i_average = np.asarray([np.NaN] * self.nrho) + t_i_average = np.asarray([np.nan] * self.nrho) else: ti_flag = 1 ti_e_flag = 0 @@ -907,14 +907,14 @@ def getti_flag(self): t_i_average = self.edge_profiles.profiles_1d[self.time_index_edge_profiles].t_i_average.value if len() < 1: logger.warning("edge_profiles.profiles_1d[:].t_i_average could not be read.") - t_i_average = np.asarray([np.NaN] * self.erho) + t_i_average = np.asarray([np.nan] * self.erho) else: ti_e_flag = 1 else: t_i_average = self.edge_profiles.ggd[self.time_index_edge_profiles].t_i_average[self.gset].values if len() < 1: logger.warning("edge_profiles.ggd[:].t_i_average could not be read.") - t_i_average = np.asarray([np.NaN] * self.erho) + t_i_average = np.asarray([np.nan] * self.erho) else: ti_e_flag = 1 @@ -927,7 +927,7 @@ def getti_flag(self): logger.warning( f"Size mismatch: rho_tor_norm = {self.nrho}, ion[{ispecies}].temperature = " f"{len(temp)}" ) - temp = np.asarray([np.NaN] * self.nrho) + temp = np.asarray([np.nan] * self.nrho) else: ti_flag = 2 if self.is_edge_profiles_present and ti_e_flag == 0: @@ -944,7 +944,7 @@ def getti_flag(self): logger.warning( f"edge_profiles.profiles_1d[:].ion[{jspecies}].temperature could not be read." ) - temperature = np.asarray([np.NaN] * self.erho) + temperature = np.asarray([np.nan] * self.erho) else: ti_e_flag = 2 else: @@ -954,7 +954,7 @@ def getti_flag(self): if len(temperature) < 1: if ti_e_flag != 1: logger.warning("edge_profiles.ggd[:].ion[:].temperature could not be read.") - temperature[self.gset].values = np.asarray([np.NaN] * self.erho) + temperature[self.gset].values = np.asarray([np.nan] * self.erho) else: ti_e_flag = 2 @@ -1032,7 +1032,7 @@ def get_ion_density(self): logger.warning( f"Size mismatch: rho_tor_norm = {self.nrho}, ion[{ispecies}].density = " f"{len(density)}" ) - density = np.asarray([np.NaN] * self.nrho) + density = np.asarray([np.nan] * self.nrho) for i in range(self.nrho): ion_density[ispecies][i] = density[i] if self.is_edge_profiles_present: @@ -1055,7 +1055,7 @@ def get_ion_density(self): logger.warning( f"edge_profiles.profiles_1d[:].ion[{jspecies}].density could not be read." ) - _density = np.asarray([np.NaN] * self.erho) + _density = np.asarray([np.nan] * self.erho) for i in range(self.erho): ion_density[ispecies][self.nrho + i] = _density[i] else: @@ -1091,7 +1091,7 @@ def get_ion_density(self): ) if len() < 1: logger.warning(f"edge_profiles.ggd[:].ion[{jspecies}.density could not be read.") - _density = np.asarray([np.NaN] * self.erho) + _density = np.asarray([np.nan] * self.erho) for i in range(self.erho): ion_density[ispecies][self.nrho + i] = _density[i] else: @@ -1140,7 +1140,7 @@ def get_v_phi_profile(self): f"Size mismatch: rho_tor_norm = {self.nrho}, ion[{ispecies}].velocity.toroidal = " f"{len(vphioid)}" ) - vphioid = np.asarray([np.NaN] * self.nrho) + vphioid = np.asarray([np.nan] * self.nrho) else: vphi_flag = 1 for i in range(self.nrho): @@ -1152,7 +1152,7 @@ def get_v_phi_profile(self): logger.warning( f"Size mismatch: rho_tor_norm = {self.nrho}, ion[{ispecies}].velocity_tor = " f"{len(vphi)}" ) - vphi = np.asarray([np.NaN] * self.nrho) + vphi = np.asarray([np.nan] * self.nrho) else: if vphi_flag == 0: vphi_flag = 2 @@ -1346,7 +1346,7 @@ def get_vpol_profile(self): f"Size mismatch: rho_tor_norm = {self.nrho}, ion[{ispecies}].velocity.poloidal =" f"{len(vpoloidal)}" ) - vpoloidal = np.asarray([np.NaN] * self.nrho) + vpoloidal = np.asarray([np.nan] * self.nrho) else: vpol_flag = 1 for i in range(self.nrho): @@ -1358,7 +1358,7 @@ def get_vpol_profile(self): logger.warning( f"Size mismatch: rho_tor_norm = {self.nrho}, ion[{ispecies}].velocity_pol = " f"{len(vpol)}" ) - vpol = np.asarray([np.NaN] * self.nrho) + vpol = np.asarray([np.nan] * self.nrho) else: if vpol_flag == 0: vpol_flag = 2 @@ -1920,7 +1920,7 @@ def get_waveform(self): # ) except Exception as e: logger.debug(f"{e}") - waveform["ti"]["central"] = [np.NaN] * len(self.time_array_core_profiles) + waveform["ti"]["central"] = [np.nan] * len(self.time_array_core_profiles) electrons_density = np.array([]) for i, _ in enumerate(self.time_array_core_profiles): @@ -2021,13 +2021,13 @@ def get_waveform(self): except Exception as e: logger.debug(f"{e}") waveform["n_species"][self.species[ispecies]]["density"]["central"] = [ - np.NaN + np.nan ] * self.common_time_length waveform["n_species"][self.species[ispecies]]["vpol"]["central"] = [ - np.NaN + np.nan ] * self.common_time_length waveform["n_species"][self.species[ispecies]]["vphi"]["central"] = [ - np.NaN + np.nan ] * self.common_time_length for itime in range(self.common_time_length): diff --git a/idstools/utils/idshelper.py b/idstools/utils/idshelper.py index aed61e8a..c4b0c6e7 100644 --- a/idstools/utils/idshelper.py +++ b/idstools/utils/idshelper.py @@ -439,7 +439,7 @@ def get_available_ids_and_times(db_entry_object) -> list: if homogeneous_time == imas.ids_defs.IDS_TIME_MODE_UNKNOWN: time_array = [] if homogeneous_time == imas.ids_defs.IDS_TIME_MODE_HETEROGENEOUS: - time_array = [np.NaN] + time_array = [np.nan] if homogeneous_time == imas.ids_defs.IDS_TIME_MODE_HOMOGENEOUS: if getattr(ids_object, "time", None): time_array = ids_object.time.value