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HDF5 generation: Don't write obsolete sens_ind (#407)
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Remove `/amiciOptions/sens_indsens_ind` which is never used. Should have been removed in
#394 already (or potentially earlier).
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dweindl authored Nov 8, 2024
1 parent b8b3ded commit f03aaf5
Showing 1 changed file with 0 additions and 13 deletions.
13 changes: 0 additions & 13 deletions python/parpe/hdf5_pe_input.py
Original file line number Diff line number Diff line change
Expand Up @@ -975,19 +975,6 @@ def _write_amici_options(self) -> None:
# set amici model options
g.attrs['nmaxevent'] = 10

num_model_parameters = \
self.f['/parameters/modelParameterNames'].shape[0]

# parameter indices w.r.t. which to compute sensitivities
# default: all
# TODO: compute only for estimated parameters
# that means, this may have to be condition-specific
# https://github.com/ICB-DCM/parPE/issues/380
self.f.require_dataset(
'/amiciOptions/sens_ind', shape=(num_model_parameters,),
dtype="<i4",
data=range(num_model_parameters))

def _get_analytically_computed_optimization_parameter_indices(self):
"""
Get optimization parameter index of all analytically computed
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