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✨ Use xarray internally and move relations/constraints/penaltys to glotaran.model #734

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merged 11 commits into from
Jul 4, 2021
Merged

✨ Use xarray internally and move relations/constraints/penaltys to glotaran.model #734

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ecbdf45
Changed calculate_matrix function to return xarrays
joernweissenborn Jun 25, 2021
622a4ea
Cleanup
joernweissenborn Jun 25, 2021
3b82f00
Added relation and constraint to basemodel
joernweissenborn Jun 25, 2021
354fc24
Added functions to apply relations and constraints
joernweissenborn Jun 25, 2021
32afedf
Removed LabelAndMatrix class
jsnel Jun 25, 2021
babf9f5
Added relations and constraints tests to base model
jsnel Jun 25, 2021
e7c4501
Added penalties to base model
joernweissenborn Jun 26, 2021
f2b9cc7
Adapted models to changes
joernweissenborn Jun 26, 2021
3d3cc89
Addressed linter issue
joernweissenborn Jun 26, 2021
6c38802
Addressed code smells
joernweissenborn Jun 26, 2021
0d301cd
Address xarray deprecation warnings
jsnel Jun 27, 2021
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53 changes: 2 additions & 51 deletions glotaran/analysis/problem.py
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Original file line number Diff line number Diff line change
Expand Up @@ -92,9 +92,7 @@ def __init__(self, scheme: Scheme):

# all of the above are always not None

self._clp_labels = None
self._matrices = None
self._reduced_clp_labels = None
self._reduced_matrices = None
self._reduced_clps = None
self._clps = None
Expand Down Expand Up @@ -166,14 +164,6 @@ def groups(self) -> dict[str, list[str]]:
self.init_bag()
return self._groups

@property
def clp_labels(
self,
) -> dict[str, list[str] | list[list[str]]]:
if self._clp_labels is None:
self.calculate_matrices()
return self._clp_labels

@property
def matrices(
self,
Expand All @@ -182,14 +172,6 @@ def matrices(
self.calculate_matrices()
return self._matrices

@property
def reduced_clp_labels(
self,
) -> dict[str, list[str] | list[list[str]]]:
if self._reduced_clp_labels is None:
self.calculate_matrices()
return self._reduced_clp_labels

@property
def reduced_matrices(
self,
Expand Down Expand Up @@ -235,23 +217,12 @@ def additional_penalty(
self,
) -> dict[str, list[float]]:
if self._additional_penalty is None:
self.calculate_additional_penalty()
self.calculate_residual()
return self._additional_penalty

@property
def full_penalty(self) -> np.ndarray:
if self._full_penalty is None:
residuals = self.weighted_residuals
additional_penalty = self.additional_penalty
if not self.grouped:
residuals = [np.concatenate(residuals[label]) for label in residuals.keys()]

self._full_penalty = (
np.concatenate((np.concatenate(residuals), additional_penalty))
if additional_penalty is not None
else np.concatenate(residuals)
)
return self._full_penalty
raise NotImplementedError

@property
def cost(self) -> float:
Expand All @@ -272,9 +243,7 @@ def reset(self):
self._reset_results()

def _reset_results(self):
self._clp_labels = None
self._matrices = None
self._reduced_clp_labels = None
self._reduced_matrices = None
self._reduced_clps = None
self._clps = None
Expand Down Expand Up @@ -372,24 +341,6 @@ def calculate_matrices(self):
def calculate_residual(self):
raise NotImplementedError

def calculate_additional_penalty(self) -> np.ndarray | dict[str, np.ndarray]:
"""Calculates additional penalties by calling the model.additional_penalty function."""
if (
callable(self.model.has_additional_penalty_function)
and self.model.has_additional_penalty_function()
):
self._additional_penalty = self.model.additional_penalty_function(
self.parameters,
self.clp_labels,
self.clps,
self.matrices,
self.data,
self._scheme.group_tolerance,
)
else:
self._additional_penalty = None
return self._additional_penalty

def create_result_data(
self, copy: bool = True, history_index: int | None = None
) -> dict[str, xr.Dataset]:
Expand Down
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