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fix/using np.nan as np.NaN was removed in the NumPy 2.0 release #16

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Merged
olivhoenen merged 1 commit into from
Mar 20, 2026
Merged

fix/using np.nan as np.NaN was removed in the NumPy 2.0 release #16

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2 changes: 1 addition & 1 deletion idstools/compute/summary.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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4 changes: 2 additions & 2 deletions idstools/domain/ecstray.py
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Expand Up @@ -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)
Expand Down
54 changes: 27 additions & 27 deletions idstools/domain/kineticprofiles.py
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Original file line number Diff line number Diff line change
Expand Up @@ -787,22 +787,22 @@ 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:
if not self.r_out_graph:
_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
Expand All @@ -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)
Expand All @@ -823,22 +823,22 @@ 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:
if not self.r_out_graph:
_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
Expand All @@ -862,22 +862,22 @@ 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:
if not self.r_out_graph:
_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
Expand All @@ -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
Expand All @@ -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

Expand All @@ -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:
Expand All @@ -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:
Expand All @@ -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

Expand Down Expand Up @@ -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:
Expand All @@ -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:
Expand Down Expand Up @@ -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:
Expand Down Expand Up @@ -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):
Expand All @@ -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
Expand Down Expand Up @@ -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):
Expand All @@ -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
Expand Down Expand Up @@ -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):
Expand Down Expand Up @@ -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):
Expand Down
2 changes: 1 addition & 1 deletion idstools/utils/idshelper.py
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Expand Up @@ -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
Expand Down
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