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Rename edata data members #3079

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Merged
FFroehlich merged 9 commits into from
Dec 2, 2025
Merged

Rename edata data members #3079

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12d5e8d
rename edata members
FFroehlich Dec 1, 2025
b2e460e
fixup
FFroehlich Dec 1, 2025
7f8a77f
fixup
FFroehlich Dec 1, 2025
924f69e
fixup doc
FFroehlich Dec 1, 2025
60e35f7
rename measurement error to noise scale
FFroehlich Dec 1, 2025
d779ec1
fixup plotting
FFroehlich Dec 1, 2025
fac0039
fixup plural
FFroehlich Dec 1, 2025
f742727
fixup + update doc
FFroehlich Dec 1, 2025
6bbcbf2
Update src/model.cpp
dweindl Dec 1, 2025
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6 changes: 3 additions & 3 deletions doc/examples/example_steady_states/ExampleEquilibrationLogic.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -470,7 +470,7 @@
"source": [
"# create edata, with 3 timepoints and 2 observables:\n",
"edata = ExpData(2, 0, 0, np.array([0.0, 0.1, 1.0]))\n",
"edata.set_observed_data([1.8] * 6)\n",
"edata.set_measurements([1.8] * 6)\n",
"edata.fixed_parameters = np.array([3.0, 5.0])\n",
"# set parameters for pre-equilibration\n",
"edata.fixed_parameters_pre_equilibration = np.array([0.0, 2.0])\n",
Expand Down Expand Up @@ -765,7 +765,7 @@
"# by setting an infinity timepoint\n",
"# and creatíng an edata object, which is needed for adjoint computation\n",
"edata = ExpData(2, 0, 0, np.array([float(\"inf\")]))\n",
"edata.set_observed_data([1.8] * 2)\n",
"edata.set_measurements([1.8] * 2)\n",
"edata.fixed_parameters = np.array([3.0, 5.0])\n",
"\n",
"model_reduced.set_steady_state_sensitivity_mode(\n",
Expand Down Expand Up @@ -853,7 +853,7 @@
"# No post-equilibration this time.\n",
"# create edata, with 3 timepoints and 2 observables:\n",
"edata = ExpData(2, 0, 0, np.array([0.0, 0.1, 1.0]))\n",
"edata.set_observed_data([1.8] * 6)\n",
"edata.set_measurements([1.8] * 6)\n",
"edata.fixed_parameters = np.array([3.0, 5.0])\n",
"# set parameters for pre-equilibration\n",
"edata.fixed_parameters_pre_equilibration = np.array([0.0, 2.0])\n",
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2 changes: 1 addition & 1 deletion doc/examples/getting_started_extended/GettingStartedExtended.ipynb
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Expand Up @@ -1135,7 +1135,7 @@
"edata.fixed_parameters = model.get_fixed_parameters()\n",
"# set sigma to 1.0 except for observable 5, so that p[7] is used instead\n",
"# (if we have sigma parameterized, the corresponding ExpData entries must NaN, otherwise they will override the parameter)\n",
"edata.set_observed_data_std_dev(\n",
"edata.set_noise_scales(\n",
" rdata[\"t\"] * 0 + np.nan,\n",
" list(model.get_observable_ids()).index(\"observable_x1withsigma\"),\n",
")\n",
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