def test_aspcap_mask(self):
self.assertEqual(np.all(aspcap_mask('C1') == aspcap_mask('ci')), True)
self.assertEqual(np.all(aspcap_mask('TIII') == aspcap_mask('ti2')), True)
# assert for example dr=1 is not supported
self.assertRaises(ValueError, aspcap_mask, 'al', 1)
# Make sure if element not found, the case is nicely handled
self.assertEqual(aspcap_mask('abc'), None)
def test_BoolMask(self):
print('==========BoolMask tests==========')
from astroNN.nn.layers import BoolMask
from astroNN.apogee import aspcap_mask
# Data preparation
random_xdata = np.random.normal(0, 1, (100, 7514))
random_ydata = np.random.normal(0, 1, (100, 25))
input = Input(shape=[7514])
dense = BoolMask(mask=aspcap_mask("Al", dr=14))(input)
output = Dense(25)(dense)
model = Model(inputs=input, outputs=output)
model.compile(optimizer='adam', loss='mse')
model.fit(random_xdata, random_ydata)
def test_BoolMask(self):
print('==========BoolMask tests==========')
from astroNN.nn.layers import BoolMask
from astroNN.apogee import aspcap_mask
# Data preparation
random_xdata = np.random.normal(0, 1, (100, 7514))
random_ydata = np.random.normal(0, 1, (100, 25))
input = Input(shape=[7514])
dense = BoolMask(mask=aspcap_mask("Al", dr=14))(input)
output = Dense(25)(dense)
model = Model(inputs=input, outputs=output)
model.compile(optimizer='adam', loss='mse')
model.fit(random_xdata, random_ydata)
# make sure a mask with all 0 raises error of invalid mask
self.assertRaises(ValueError, BoolMask, np.zeros(7514))
def model(self):
input_tensor = Input(shape=self._input_shape, name='input')
input_tensor_flattened = Flatten()(input_tensor)
labels_err_tensor = Input(shape=(self._labels_shape, ),
name='labels_err')
# slice spectra to censor out useless region for elements
censored_c_input = BoolMask(aspcap_mask("C", dr=14),
name='C_Mask')(input_tensor_flattened)
censored_c1_input = BoolMask(aspcap_mask("C1", dr=14),
name='C1_Mask')(input_tensor_flattened)
censored_n_input = BoolMask(aspcap_mask("N", dr=14),
name='N_Mask')(input_tensor_flattened)
censored_o_input = BoolMask(aspcap_mask("O", dr=14),
name='O_Mask')(input_tensor_flattened)
censored_na_input = BoolMask(aspcap_mask("Na", dr=14),
name='Na_Mask')(input_tensor_flattened)
censored_mg_input = BoolMask(aspcap_mask("Mg", dr=14),
name='Mg_Mask')(input_tensor_flattened)
censored_al_input = BoolMask(aspcap_mask("Al", dr=14),
name='Al_Mask')(input_tensor_flattened)
censored_si_input = BoolMask(aspcap_mask("Si", dr=14),
name='Si_Mask')(input_tensor_flattened)
censored_p_input = BoolMask(aspcap_mask("P", dr=14),
name='P_Mask')(input_tensor_flattened)
censored_s_input = BoolMask(aspcap_mask("S", dr=14),
name='S_Mask')(input_tensor_flattened)
censored_k_input = BoolMask(aspcap_mask("K", dr=14),
name='K_Mask')(input_tensor_flattened)
censored_ca_input = BoolMask(aspcap_mask("Ca", dr=14),
name='Ca_Mask')(input_tensor_flattened)
censored_ti_input = BoolMask(aspcap_mask("Ti", dr=14),
name='Ti_Mask')(input_tensor_flattened)
censored_ti2_input = BoolMask(aspcap_mask("Ti2", dr=14),
name='Ti2_Mask')(input_tensor_flattened)
censored_v_input = BoolMask(aspcap_mask("V", dr=14),
name='V_Mask')(input_tensor_flattened)
censored_cr_input = BoolMask(aspcap_mask("Cr", dr=14),
name='Cr_Mask')(input_tensor_flattened)
censored_mn_input = BoolMask(aspcap_mask("Mn", dr=14),
name='Mn_Mask')(input_tensor_flattened)
censored_co_input = BoolMask(aspcap_mask("Co", dr=14),
name='Co_Mask')(input_tensor_flattened)
censored_ni_input = BoolMask(aspcap_mask("Ni", dr=14),
name='Ni_Mask')(input_tensor_flattened)
# get neurones from each elements from censored spectra
c_dense = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[2] * 8,
kernel_initializer=self.initializer,
name='c_dense',
activation=self.activation,
kernel_regularizer=regularizers.l2(
self.l2))(censored_c_input))
c1_dense = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[2],
kernel_initializer=self.initializer,
name='c1_dense',
activation=self.activation,
kernel_regularizer=regularizers.l2(
self.l2))(censored_c1_input))
n_dense = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[2] * 8,
kernel_initializer=self.initializer,
name='n_dense',
activation=self.activation,
kernel_regularizer=regularizers.l2(
self.l2))(censored_n_input))
o_dense = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[2],
kernel_initializer=self.initializer,
name='o_dense',
activation=self.activation,
kernel_regularizer=regularizers.l2(
self.l2))(censored_o_input))
na_dense = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[2],
kernel_initializer=self.initializer,
name='na_dense',
activation=self.activation,
kernel_regularizer=regularizers.l2(
self.l2))(censored_na_input))
mg_dense = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[2],
kernel_initializer=self.initializer,
name='mg_dense',
activation=self.activation,
kernel_regularizer=regularizers.l2(
self.l2))(censored_mg_input))
al_dense = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[2],
kernel_initializer=self.initializer,
name='al_dense',
activation=self.activation,
kernel_regularizer=regularizers.l2(
self.l2))(censored_al_input))
si_dense = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[2],
kernel_initializer=self.initializer,
name='si_dense',
activation=self.activation,
kernel_regularizer=regularizers.l2(
self.l2))(censored_si_input))
p_dense = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[2],
kernel_initializer=self.initializer,
name='p_dense',
activation=self.activation,
kernel_regularizer=regularizers.l2(
self.l2))(censored_p_input))
s_dense = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[2],
kernel_initializer=self.initializer,
name='s_dense',
activation=self.activation,
kernel_regularizer=regularizers.l2(
self.l2))(censored_s_input))
k_dense = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[2],
kernel_initializer=self.initializer,
name='k_dense',
activation=self.activation,
kernel_regularizer=regularizers.l2(
self.l2))(censored_k_input))
ca_dense = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[2],
kernel_initializer=self.initializer,
name='ca_dense',
activation=self.activation,
kernel_regularizer=regularizers.l2(
self.l2))(censored_ca_input))
ti_dense = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[2],
kernel_initializer=self.initializer,
name='ti_dense',
activation=self.activation,
kernel_regularizer=regularizers.l2(
self.l2))(censored_ti_input))
ti2_dense = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[2],
kernel_initializer=self.initializer,
name='ti2_dense',
activation=self.activation,
kernel_regularizer=regularizers.l2(
self.l2))(censored_ti2_input))
v_dense = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[2],
kernel_initializer=self.initializer,
name='v_dense',
activation=self.activation,
kernel_regularizer=regularizers.l2(
self.l2))(censored_v_input))
cr_dense = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[2],
kernel_initializer=self.initializer,
name='cr_dense',
activation=self.activation,
kernel_regularizer=regularizers.l2(
self.l2))(censored_cr_input))
mn_dense = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[2],
kernel_initializer=self.initializer,
name='mn_dense',
activation=self.activation,
kernel_regularizer=regularizers.l2(
self.l2))(censored_mn_input))
co_dense = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[2],
kernel_initializer=self.initializer,
name='co_dense',
activation=self.activation,
kernel_regularizer=regularizers.l2(
self.l2))(censored_co_input))
ni_dense = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[2],
kernel_initializer=self.initializer,
name='ni_dense',
activation=self.activation,
kernel_regularizer=regularizers.l2(
self.l2))(censored_ni_input))
# get neurones from each elements from censored spectra
c_dense_2 = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[3] * 4,
kernel_initializer=self.initializer,
activation=self.activation,
name='c_dense_2')(c_dense))
c1_dense_2 = MCDropout(self.dropout_rate,
disable=self.disable_dropout)(Dense(
units=self.num_hidden[3],
kernel_initializer=self.initializer,
activation=self.activation,
name='c1_dense_2')(c1_dense))
n_dense_2 = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[3] * 4,
kernel_initializer=self.initializer,
activation=self.activation,
name='n_dense_2')(n_dense))
o_dense_2 = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[3],
kernel_initializer=self.initializer,
activation=self.activation,
name='o_dense_2')(o_dense))
na_dense_2 = MCDropout(self.dropout_rate,
disable=self.disable_dropout)(Dense(
units=self.num_hidden[3],
kernel_initializer=self.initializer,
activation=self.activation,
name='na_dense_2')(na_dense))
mg_dense_2 = MCDropout(self.dropout_rate,
disable=self.disable_dropout)(Dense(
units=self.num_hidden[3],
kernel_initializer=self.initializer,
activation=self.activation,
name='mg_dense_2')(mg_dense))
al_dense_2 = MCDropout(self.dropout_rate,
disable=self.disable_dropout)(Dense(
units=self.num_hidden[3],
kernel_initializer=self.initializer,
activation=self.activation,
name='al_dense_2')(al_dense))
si_dense_2 = MCDropout(self.dropout_rate,
disable=self.disable_dropout)(Dense(
units=self.num_hidden[3],
kernel_initializer=self.initializer,
activation=self.activation,
name='si_dense_2')(si_dense))
p_dense_2 = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[3],
kernel_initializer=self.initializer,
activation=self.activation,
name='p_dense_2')(p_dense))
s_dense_2 = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[3],
kernel_initializer=self.initializer,
activation=self.activation,
name='s_dense_2')(s_dense))
k_dense_2 = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[3],
kernel_initializer=self.initializer,
activation=self.activation,
name='k_dense_2')(k_dense))
ca_dense_2 = MCDropout(self.dropout_rate,
disable=self.disable_dropout)(Dense(
units=self.num_hidden[3],
kernel_initializer=self.initializer,
activation=self.activation,
name='ca_dense_2')(ca_dense))
ti_dense_2 = MCDropout(self.dropout_rate,
disable=self.disable_dropout)(Dense(
units=self.num_hidden[3],
kernel_initializer=self.initializer,
activation=self.activation,
name='ti_dense_2')(ti_dense))
ti2_dense_2 = MCDropout(self.dropout_rate,
disable=self.disable_dropout)(Dense(
units=self.num_hidden[3],
kernel_initializer=self.initializer,
activation=self.activation,
name='ti2_dense_2')(ti2_dense))
v_dense_2 = MCDropout(self.dropout_rate, disable=self.disable_dropout)(
Dense(units=self.num_hidden[3],
kernel_initializer=self.initializer,
activation=self.activation,
name='v_dense_2')(v_dense))
cr_dense_2 = MCDropout(self.dropout_rate,
disable=self.disable_dropout)(Dense(
units=self.num_hidden[3],
kernel_initializer=self.initializer,
activation=self.activation,
name='cr_dense_2')(cr_dense))
mn_dense_2 = MCDropout(self.dropout_rate,
disable=self.disable_dropout)(Dense(
units=self.num_hidden[3],
kernel_initializer=self.initializer,
activation=self.activation,
name='mn_dense_2')(mn_dense))
co_dense_2 = MCDropout(self.dropout_rate,
disable=self.disable_dropout)(Dense(
units=self.num_hidden[3],
kernel_initializer=self.initializer,
activation=self.activation,
name='co_dense_2')(co_dense))
ni_dense_2 = MCDropout(self.dropout_rate,
disable=self.disable_dropout)(Dense(
units=self.num_hidden[3],
kernel_initializer=self.initializer,
activation=self.activation,
name='ni_dense_2')(ni_dense))
# Basically the same as ApogeeBCNN structure
cnn_layer_1 = Conv1D(kernel_initializer=self.initializer,
padding="same",
filters=self.num_filters[0],
kernel_size=self.filter_len,
kernel_regularizer=regularizers.l2(
self.l2))(input_tensor)
activation_1 = Activation(activation=self.activation)(cnn_layer_1)
dropout_1 = MCDropout(self.dropout_rate,
disable=self.disable_dropout)(activation_1)
cnn_layer_2 = Conv1D(kernel_initializer=self.initializer,
padding="same",
filters=self.num_filters[1],
kernel_size=self.filter_len,
kernel_regularizer=regularizers.l2(
self.l2))(dropout_1)
activation_2 = Activation(activation=self.activation)(cnn_layer_2)
maxpool_1 = MaxPooling1D(pool_size=self.pool_length)(activation_2)
flattener = Flatten()(maxpool_1)
dropout_2 = MCDropout(self.dropout_rate,
disable=self.disable_dropout)(flattener)
layer_3 = Dense(units=self.num_hidden[0],
kernel_regularizer=regularizers.l2(self.l2),
kernel_initializer=self.initializer)(dropout_2)
activation_3 = Activation(activation=self.activation)(layer_3)
dropout_3 = MCDropout(self.dropout_rate,
disable=self.disable_dropout)(activation_3)
layer_4 = Dense(units=self.num_hidden[1],
kernel_regularizer=regularizers.l2(self.l2),
kernel_initializer=self.initializer)(dropout_3)
activation_4 = Activation(activation=self.activation)(layer_4)
teff_output = Dense(units=1)(activation_4)
logg_output = Dense(units=1)(activation_4)
fe_output = Dense(units=1)(activation_4)
old_3_output_wo_grad = StopGrad()(concatenate(
[teff_output, logg_output, fe_output]))
teff_output_var = Dense(units=1)(activation_4)
logg_output_var = Dense(units=1)(activation_4)
fe_output_var = Dense(units=1)(activation_4)
aux_fullspec = Dense(units=self.num_hidden[4],
kernel_initializer=self.initializer,
kernel_constraint=MaxNorm(self.maxnorm),
name='aux_fullspec')(activation_4)
fullspec_hidden = concatenate([aux_fullspec, old_3_output_wo_grad])
# get the final answer
c_concat = Dense(units=1, name='c_concat')(concatenate(
[c_dense_2, fullspec_hidden]))
c1_concat = Dense(units=1, name='c1_concat')(concatenate(
[c1_dense_2, fullspec_hidden]))
n_concat = Dense(units=1, name='n_concat')(concatenate(
[n_dense_2, fullspec_hidden]))
o_concat = Dense(units=1, name='o_concat')(concatenate(
[o_dense_2, fullspec_hidden]))
na_concat = Dense(units=1, name='na_concat')(concatenate(
[na_dense_2, fullspec_hidden]))
mg_concat = Dense(units=1, name='mg_concat')(concatenate(
[mg_dense_2, fullspec_hidden]))
al_concat = Dense(units=1, name='al_concat')(concatenate(
[al_dense_2, fullspec_hidden]))
si_concat = Dense(units=1, name='si_concat')(concatenate(
[si_dense_2, fullspec_hidden]))
p_concat = Dense(units=1, name='p_concat')(concatenate(
[p_dense_2, fullspec_hidden]))
s_concat = Dense(units=1, name='s_concat')(concatenate(
[s_dense_2, fullspec_hidden]))
k_concat = Dense(units=1, name='k_concat')(concatenate(
[k_dense_2, fullspec_hidden]))
ca_concat = Dense(units=1, name='ca_concat')(concatenate(
[ca_dense_2, fullspec_hidden]))
ti_concat = Dense(units=1, name='ti_concat')(concatenate(
[ti_dense_2, fullspec_hidden]))
ti2_concat = Dense(units=1, name='ti2_concat')(concatenate(
[ti2_dense_2, fullspec_hidden]))
v_concat = Dense(units=1, name='v_concat')(concatenate(
[v_dense_2, fullspec_hidden]))
cr_concat = Dense(units=1, name='cr_concat')(concatenate(
[cr_dense_2, fullspec_hidden]))
mn_concat = Dense(units=1, name='mn_concat')(concatenate(
[mn_dense_2, fullspec_hidden]))
co_concat = Dense(units=1, name='co_concat')(concatenate(
[co_dense_2, fullspec_hidden]))
ni_concat = Dense(units=1, name='ni_concat')(concatenate(
[ni_dense_2, fullspec_hidden]))
# get the final predictive uncertainty
c_concat_var = Dense(units=1, name='c_concat_var')(concatenate(
[c_dense_2, fullspec_hidden]))
c1_concat_var = Dense(units=1, name='c1_concat_var')(concatenate(
[c1_dense_2, fullspec_hidden]))
n_concat_var = Dense(units=1, name='n_concat_var')(concatenate(
[n_dense_2, fullspec_hidden]))
o_concat_var = Dense(units=1, name='o_concat_var')(concatenate(
[o_dense_2, fullspec_hidden]))
na_concat_var = Dense(units=1, name='na_concat_var')(concatenate(
[na_dense_2, fullspec_hidden]))
mg_concat_var = Dense(units=1, name='mg_concat_var')(concatenate(
[mg_dense_2, fullspec_hidden]))
al_concat_var = Dense(units=1, name='al_concat_var')(concatenate(
[al_dense_2, fullspec_hidden]))
si_concat_var = Dense(units=1, name='si_concat_var')(concatenate(
[si_dense_2, fullspec_hidden]))
p_concat_var = Dense(units=1, name='p_concat_var')(concatenate(
[p_dense_2, fullspec_hidden]))
s_concat_var = Dense(units=1, name='s_concat_var')(concatenate(
[s_dense_2, fullspec_hidden]))
k_concat_var = Dense(units=1, name='k_concat_var')(concatenate(
[k_dense_2, fullspec_hidden]))
ca_concat_var = Dense(units=1, name='ca_concat_var')(concatenate(
[ca_dense_2, fullspec_hidden]))
ti_concat_var = Dense(units=1, name='ti_concat_var')(concatenate(
[ti_dense_2, fullspec_hidden]))
ti2_concat_var = Dense(units=1, name='ti2_concat_var')(concatenate(
[ti2_dense_2, fullspec_hidden]))
v_concat_var = Dense(units=1, name='v_concat_var')(concatenate(
[v_dense_2, fullspec_hidden]))
cr_concat_var = Dense(units=1, name='cr_concat_var')(concatenate(
[cr_dense_2, fullspec_hidden]))
mn_concat_var = Dense(units=1, name='mn_concat_var')(concatenate(
[mn_dense_2, fullspec_hidden]))
co_concat_var = Dense(units=1, name='co_concat_var')(concatenate(
[co_dense_2, fullspec_hidden]))
ni_concat_var = Dense(units=1, name='ni_concat_var')(concatenate(
[ni_dense_2, fullspec_hidden]))
# concatenate answer
output = concatenate([
teff_output, logg_output, c_concat, c1_concat, n_concat, o_concat,
na_concat, mg_concat, al_concat, si_concat, p_concat, s_concat,
k_concat, ca_concat, ti_concat, ti2_concat, v_concat, cr_concat,
mn_concat, fe_output, co_concat, ni_concat
],
name='output')
# concatenate predictive uncertainty
variance_output = concatenate([
teff_output_var, logg_output_var, c_concat_var, c1_concat_var,
n_concat_var, o_concat_var, na_concat_var, mg_concat_var,
al_concat_var, si_concat_var, p_concat_var, s_concat_var,
k_concat_var, ca_concat_var, ti_concat_var, ti2_concat_var,
v_concat_var, cr_concat_var, mn_concat_var, fe_output_var,
co_concat_var, ni_concat_var
],
name='variance_output')
model = Model(inputs=[input_tensor, labels_err_tensor],
outputs=[output, variance_output])
# new astroNN high performance dropout variational inference on GPU expects single output
model_prediction = Model(inputs=input_tensor,
outputs=concatenate([output,
variance_output]))
variance_loss = mse_var_wrapper(output, labels_err_tensor)
output_loss = mse_lin_wrapper(variance_output, labels_err_tensor)
return model, model_prediction, output_loss, variance_loss