HDF5 input file organization

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Daniel Weindl edited this page Jun 20, 2017 · 1 revision

MultiConditionProblem expects HDF5 input files with the following format:

/measurements/y: ny * numExperiments
/measurements/sigmay: ny * numExperiments
/fixedParameters: nk * numExperiments
/amiciOptions: Options for AMICI -> as in amioptions() in matlab
/multiStartOptions: numMultiStarts
/optimizationOptions:
- maxIter
- numStarts
- retryOptimization
- functionTolerance

Ordering of fixed parameters and and measurements as in processed AMICI _syms file.

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