def _calculate_residual(self, label: str, dataset_model: DatasetModel):
self._group._reduced_clps[label] = []
self._group._clps[label] = []
self._group._weighted_residuals[label] = []
self._group._residuals[label] = []
data = dataset_model.get_data()
global_axis = dataset_model.get_global_axis()
for i, index in enumerate(global_axis):
reduced_clp_labels, reduced_matrix = (
self._group.reduced_matrices[label][i]
if dataset_model.is_index_dependent() else
self._group.reduced_matrices[label])
if not dataset_model.is_index_dependent():
reduced_matrix = reduced_matrix.copy()
if dataset_model.scale is not None:
reduced_matrix *= dataset_model.scale
weight = dataset_model.get_weight()
if weight is not None:
apply_weight(reduced_matrix, weight[:, i])
reduced_clps, residual = self._group._residual_function(
reduced_matrix, data[:, i])
self._group._reduced_clps[label].append(reduced_clps)
clp_labels = self._get_clp_labels(label, i)
self._group._clps[label].append(
retrieve_clps(
self._group.model,
self._group.parameters,
clp_labels,
reduced_clp_labels,
reduced_clps,
index,
))
self._group._weighted_residuals[label].append(residual)
if weight is not None:
self._group._residuals[label].append(residual / weight[:, i])
else:
self._group._residuals[label].append(residual)
clp_labels = self._get_clp_labels(label)
additional_penalty = calculate_clp_penalties(
self._group.model,
self._group.parameters,
clp_labels,
self._group._clps[label],
global_axis,
self._group.dataset_models,
)
if additional_penalty.size != 0:
self._group._additional_penalty.append(additional_penalty)
def _calculate_full_model_residual(self, label: str,
dataset_model: DatasetModel):
model_matrix = self._group.matrices[label]
global_matrix = self.global_matrices[label].matrix
if dataset_model.is_index_dependent():
matrix = np.concatenate([
np.kron(global_matrix[i, :], model_matrix[i].matrix)
for i in range(global_matrix.shape[0])
])
else:
matrix = np.kron(global_matrix, model_matrix.matrix)
weight = self._flattened_weights.get(label)
if weight is not None:
apply_weight(matrix, weight)
data = self._flattened_data[label]
(
self._group._clps[label],
self._group._weighted_residuals[label],
) = self._group._residual_function(matrix, data)
self._group._residuals[label] = self._group._weighted_residuals[label]
if weight is not None:
self._group._residuals[label] /= weight
def finalize_data(
self,
dataset_model: DatasetModel,
dataset: xr.Dataset,
is_full_model: bool = False,
as_global: bool = False,
):
if not is_full_model:
global_dimension = dataset_model.get_global_dimension()
model_dimension = dataset_model.get_model_dimension()
dataset.coords["coherent_artifact_order"] = np.arange(
1, self.order + 1)
response_dimensions = (model_dimension, "coherent_artifact_order")
if dataset_model.is_index_dependent() is True:
response_dimensions = (global_dimension, *response_dimensions)
dataset["coherent_artifact_response"] = (
response_dimensions,
dataset.matrix.sel(clp_label=self.compartments()).values,
)
dataset["coherent_artifact_associated_spectra"] = (
(global_dimension, "coherent_artifact_order"),
dataset.clp.sel(clp_label=self.compartments()).values,
)
retrieve_irf(dataset_model, dataset,
dataset_model.get_global_dimension())
def simulate_clp(
dataset_model: DatasetModel,
parameters: ParameterGroup,
clp: xr.DataArray,
):
if "clp_label" not in clp.coords:
raise ValueError("Missing coordinate 'clp_label' in clp.")
global_dimension = next(dim for dim in clp.coords if dim != "clp_label")
global_axis = clp.coords[global_dimension]
matrices = ([
calculate_matrix(
dataset_model,
{global_dimension: index},
) for index, _ in enumerate(global_axis)
] if dataset_model.is_index_dependent() else calculate_matrix(
dataset_model, {}))
model_dimension = dataset_model.get_model_dimension()
model_axis = dataset_model.get_coordinates()[model_dimension]
result = xr.DataArray(
data=0.0,
coords=[
(model_dimension, model_axis.data),
(global_dimension, global_axis.data),
],
)
result = result.to_dataset(name="data")
for i in range(global_axis.size):
index_matrix = matrices[i] if dataset_model.is_index_dependent(
) else matrices
result.data[:, i] = np.dot(
index_matrix.matrix,
clp.isel({
global_dimension: i
}).sel({"clp_label": index_matrix.clp_labels}),
)
return result