The problem of an optimal mapping between Hilbert spaces $IN$ of $\left|ψ\right\rangle$ and $OUT$ of $\left|φ\right\rangle$ based on a set of wavefunction measurements (within a phase) $ψ_l \to φ_l$, $l=1\dots M$, is formulated as an optimization problem maximizing the total fidelity $\sum_{l=1}^{M} ω^{(l)} \left|\langleφ_l|\mathcal{U}|ψ_l\rangle\right|^2$ subject to probability preservation constraints on $\mathcal{U}$ (partial unitarity). The constructed operator $\mathcal{U}$ can be considered as an $IN$ to $OUT$ quantum channel; it is a partially unitary rectangular matrix (an isometry) of dimension $\dim(OUT) \times \dim(IN)$ transforming operators as $A^{OUT}=\mathcal{U} A^{IN} \mathcal{U}^{\dagger}$. An iterative algorithm for finding the global maximum of this optimization problem is developed, and its application to a number of problems is demonstrated. A software product implementing the algorithm is available from the authors.