diff --git a/tardis/io/configuration/tests/data/tardis_configv1_verysimple.yml b/tardis/io/configuration/tests/data/tardis_configv1_verysimple.yml index f165578f493..ef139d0f1d4 100644 --- a/tardis/io/configuration/tests/data/tardis_configv1_verysimple.yml +++ b/tardis/io/configuration/tests/data/tardis_configv1_verysimple.yml @@ -47,3 +47,5 @@ spectrum: start: 500 angstrom stop: 20000 angstrom num: 10000 + virtual: + virtual_packet_logging: True diff --git a/tardis/io/model/readers/cmfgen.py b/tardis/io/model/readers/cmfgen.py index 3ab63589a36..563330fdd59 100644 --- a/tardis/io/model/readers/cmfgen.py +++ b/tardis/io/model/readers/cmfgen.py @@ -65,7 +65,7 @@ def read_cmfgen_model(fname): metadata["t0"] = float(metadata["t0"]) * u.day data = pd.read_csv( fname, - delim_whitespace=True, + sep=r"\s+", skiprows=DATA_START_ROW, header=None, index_col=0, diff --git a/tardis/io/util.py b/tardis/io/util.py index 8d1e1e9de12..e0cdc1079c0 100644 --- a/tardis/io/util.py +++ b/tardis/io/util.py @@ -266,14 +266,18 @@ def to_hdf_util( if value.ndim == 1: # This try,except block is only for model.plasma.levels try: - pd.Series(value).to_hdf(buf, os.path.join(path, key)) + pd.Series(value).to_hdf( + buf, key=os.path.join(path, key) + ) except NotImplementedError: logger.debug( "Could not convert SERIES to HDF. Converting DATAFRAME to HDF" ) - pd.DataFrame(value).to_hdf(buf, os.path.join(path, key)) + pd.DataFrame(value).to_hdf( + buf, key=os.path.join(path, key) + ) else: - pd.DataFrame(value).to_hdf(buf, os.path.join(path, key)) + pd.DataFrame(value).to_hdf(buf, key=os.path.join(path, key)) else: # value is a TARDIS object like model, transport or plasma try: value.to_hdf(buf, path, name=key, overwrite=overwrite) @@ -282,10 +286,10 @@ def to_hdf_util( "Could not convert VALUE to HDF. Converting DATA (Dataframe) to HDF" ) data = pd.DataFrame([value]) - data.to_hdf(buf, os.path.join(path, key)) + data.to_hdf(buf, key=os.path.join(path, key)) if scalars: - pd.Series(scalars).to_hdf(buf, os.path.join(path, "scalars")) + pd.Series(scalars).to_hdf(buf, key=os.path.join(path, "scalars")) if buf.is_open: buf.close() diff --git a/tardis/plasma/properties/helium_nlte.py b/tardis/plasma/properties/helium_nlte.py index cd05ce73327..32dc3716f12 100644 --- a/tardis/plasma/properties/helium_nlte.py +++ b/tardis/plasma/properties/helium_nlte.py @@ -43,14 +43,18 @@ def calculate( he_one_population = HeliumNLTE.calculate_helium_one( g_electron, beta_rad, ionization_data, level_boltzmann_factor, g, w ) - helium_population.loc[0].update(he_one_population) + helium_population.loc[ + 0, helium_population.columns + ] = he_one_population.values # He I ground state helium_population.loc[0, 0] = 0.0 # He II excited states he_two_population = level_boltzmann_factor.loc[2, 1].mul( (float(g.loc[2, 1, 0]) ** (-1.0)) ) - helium_population.loc[1].update(he_two_population) + helium_population.loc[ + 1, helium_population.columns + ] = he_two_population.values # He II ground state helium_population.loc[1, 0] = 1.0 # He III states diff --git a/tardis/plasma/properties/ion_population.py b/tardis/plasma/properties/ion_population.py index 1d342163e21..e5eef7253a0 100644 --- a/tardis/plasma/properties/ion_population.py +++ b/tardis/plasma/properties/ion_population.py @@ -434,8 +434,12 @@ def update_he_population( he_three_population = helium_population_updated.loc[2].mul( 1.0 / n_electron ) - helium_population_updated.loc[0].update(he_one_population) - helium_population_updated.loc[2].update(he_three_population) + helium_population_updated.loc[ + 0, helium_population_updated.columns + ] = he_one_population.values + helium_population_updated.loc[ + 2, helium_population_updated.columns + ] = he_three_population.values unnormalised = helium_population_updated.sum() normalised = helium_population_updated.mul( number_density.loc[2] / unnormalised @@ -465,15 +469,15 @@ def calculate( helium_population_updated = self.update_he_population( helium_population, n_electron, number_density ) - ion_number_density.loc[2, 0].update( - helium_population_updated.loc[0].sum(axis=0) - ) - ion_number_density.loc[2, 1].update( - helium_population_updated.loc[1].sum(axis=0) - ) - ion_number_density.loc[2, 2].update( - helium_population_updated.loc[2, 0] - ) + ion_number_density.loc[2, 0] = helium_population_updated.loc[ + 0 + ].sum(axis=0) + ion_number_density.loc[2, 1] = helium_population_updated.loc[ + 1 + ].sum(axis=0) + ion_number_density.loc[2, 2] = helium_population_updated.loc[ + 2, 0 + ] ion_numbers = ion_number_density.index.get_level_values( 1 ).values diff --git a/tardis/plasma/properties/level_population.py b/tardis/plasma/properties/level_population.py index 09ec8c3853e..5169b047258 100644 --- a/tardis/plasma/properties/level_population.py +++ b/tardis/plasma/properties/level_population.py @@ -98,5 +98,7 @@ def calculate( partition_function, ) if helium_population_updated is not None: - level_number_density.loc[2].update(helium_population_updated) + level_number_density.loc[ + 2, helium_population_updated.columns + ] = helium_population_updated.values return level_number_density diff --git a/tardis/plasma/properties/partition_function.py b/tardis/plasma/properties/partition_function.py index 0fafaeee976..26d4c1f8dc4 100644 --- a/tardis/plasma/properties/partition_function.py +++ b/tardis/plasma/properties/partition_function.py @@ -251,7 +251,7 @@ def _main_nlte_calculation( ) else: raise e - general_level_boltzmann_factor[i].loc[species] = ( + general_level_boltzmann_factor.loc[species, i] = ( level_boltzmann_factor * g.loc[species][0] / level_boltzmann_factor[0] diff --git a/tardis/spectrum/tests/test_spectrum.py b/tardis/spectrum/tests/test_spectrum.py index e23badeff42..31bf47e6fa9 100644 --- a/tardis/spectrum/tests/test_spectrum.py +++ b/tardis/spectrum/tests/test_spectrum.py @@ -78,7 +78,9 @@ def test_flux_nu(spectrum): ) else: with pytest.raises(AttributeError): - spectrum.flux_nu + spectrum.luminosity_to_flux( + spectrum.luminosity_density_nu, spectrum.distance + ) def test_flux_lambda(spectrum): @@ -93,7 +95,9 @@ def test_flux_lambda(spectrum): ) else: with pytest.raises(AttributeError): - spectrum.flux_nu + spectrum.luminosity_to_flux( + spectrum.luminosity_density_nu, spectrum.distance + ) ### diff --git a/tardis/visualization/tools/convergence_plot.py b/tardis/visualization/tools/convergence_plot.py index baac3ea0722..b4a9438840e 100644 --- a/tardis/visualization/tools/convergence_plot.py +++ b/tardis/visualization/tools/convergence_plot.py @@ -28,7 +28,7 @@ def transition_colors(length, name="jet"): ------- colors: list """ - cmap = mpl.cm.get_cmap(name, length) + cmap = mpl.pyplot.get_cmap(name, length) colors = [] for i in range(cmap.N): rgb = cmap(i)[:3] diff --git a/tardis/visualization/tools/liv_plot.py b/tardis/visualization/tools/liv_plot.py index ee14697ad83..0b88dd975cc 100644 --- a/tardis/visualization/tools/liv_plot.py +++ b/tardis/visualization/tools/liv_plot.py @@ -311,7 +311,7 @@ def _prepare_plot_data( raise ValueError("No valid species found for plotting.") self._make_colorbar_labels() - self.cmap = cm.get_cmap(cmapname, len(self._species_name)) + self.cmap = plt.get_cmap(cmapname, len(self._species_name)) self._make_colorbar_colors() if packet_wvl_range is None: diff --git a/tardis/visualization/tools/sdec_plot.py b/tardis/visualization/tools/sdec_plot.py index e306f141be5..2ca12fbb06f 100644 --- a/tardis/visualization/tools/sdec_plot.py +++ b/tardis/visualization/tools/sdec_plot.py @@ -1229,7 +1229,7 @@ def generate_plot_mpl( # Get the labels in the color bar. This determines the number of unique colors self._make_colorbar_labels() # Set colormap to be used in elements of emission and absorption plots - self.cmap = cm.get_cmap(cmapname, len(self._species_name)) + self.cmap = plt.get_cmap(cmapname, len(self._species_name)) # Get the number of unqie colors self._make_colorbar_colors() self._show_colorbar_mpl() @@ -1629,7 +1629,7 @@ def generate_plot_ply( # Get the labels in the color bar. This determines the number of unique colors self._make_colorbar_labels() # Set colormap to be used in elements of emission and absorption plots - self.cmap = cm.get_cmap(cmapname, len(self._species_name)) + self.cmap = plt.get_cmap(cmapname, len(self._species_name)) # Get the number of unique colors self._make_colorbar_colors()